diff --git a/code/missioneditor/sexp_tree_actions.cpp b/code/missioneditor/sexp_tree_actions.cpp
index b5820663895..5807495cd1e 100644
--- a/code/missioneditor/sexp_tree_actions.cpp
+++ b/code/missioneditor/sexp_tree_actions.cpp
@@ -13,6 +13,12 @@ SexpTreeActions::SexpTreeActions(SexpTreeModel& model, ISexpTreeUI& ui)
 {
 }
 
+void SexpTreeActions::set_node_flags(int node_index, int flags)
+{
+	_model.tree_nodes[node_index].flags = flags;
+	_ui.ui_set_item_editable(_model.tree_nodes[node_index].handle, (flags & EDITABLE) != 0);
+}
+
 // Free all children of a node from both the model and the UI widget.
 // After this call, the node has no children in either layer.
 void SexpTreeActions::clear_node_children(int node_index)
@@ -52,7 +58,7 @@ void SexpTreeActions::replace_data(const char* data, int type)
 	_ui.ui_set_item_text(h, data);
 	NodeImage bmap = _model.get_data_image(node_idx);
 	_ui.ui_set_item_image(h, bmap);
-	_model.tree_nodes[node_idx].flags = EDITABLE;
+	set_node_flags(node_idx, EDITABLE);
 
 	// check remaining data beyond replaced data for validity
 	verify_and_fix_arguments(_model.tree_nodes[node_idx].parent);
@@ -82,7 +88,7 @@ void SexpTreeActions::replace_variable_data(int var_idx, int type)
 	void* h = _model.tree_nodes[node_idx].handle;
 	_ui.ui_set_item_text(h, buf);
 	_ui.ui_set_item_image(h, NodeImage::VARIABLE);
-	_model.tree_nodes[node_idx].flags = NOT_EDITABLE;
+	set_node_flags(node_idx, NOT_EDITABLE);
 
 	// check remaining data beyond replaced data for validity
 	verify_and_fix_arguments(_model.tree_nodes[node_idx].parent);
@@ -105,7 +111,7 @@ void SexpTreeActions::replace_container_name(const sexp_container& container)
 	void* h = _model.tree_nodes[node_idx].handle;
 	_ui.ui_set_item_image(h, NodeImage::CONTAINER_NAME);
 	_ui.ui_set_item_text(h, container.container_name.c_str());
-	_model.tree_nodes[node_idx].flags = NOT_EDITABLE;
+	set_node_flags(node_idx, NOT_EDITABLE);
 
 	if (_model.modified)
 		*_model.modified = 1;
@@ -151,7 +157,7 @@ void SexpTreeActions::replace_container_data(const sexp_container& container,
 	void* h = _model.tree_nodes[node_idx].handle;
 	_ui.ui_set_item_image(h, NodeImage::CONTAINER_DATA);
 	_ui.ui_set_item_text(h, container.container_name.c_str());
-	_model.tree_nodes[node_idx].flags = NOT_EDITABLE;
+	set_node_flags(node_idx, NOT_EDITABLE);
 
 	if (set_default_modifier) {
 		add_default_modifier(container);
@@ -174,7 +180,7 @@ void SexpTreeActions::replace_operator(const char* op)
 	_model.set_node(node_idx, (SEXPT_OPERATOR | SEXPT_VALID), op);
 	void* h = _model.tree_nodes[node_idx].handle;
 	_ui.ui_set_item_text(h, op);
-	_model.tree_nodes[node_idx].flags = OPERAND;
+	set_node_flags(node_idx, OPERAND);
 
 	if (_model.modified)
 		*_model.modified = 1;
@@ -207,10 +213,10 @@ void SexpTreeActions::expand_operator(int node)
 		Assertion(_model.tree_nodes[data].child == -1, "Child %d of node %d unexpectedly has its own children (child %d)", data, node, _model.tree_nodes[data].child);
 
 		_ui.ui_set_item_text(h, _model.tree_nodes[node].text);
-		_model.tree_nodes[node].flags = OPERAND;
+		set_node_flags(node, OPERAND);
 		NodeImage bmap = _model.get_data_image(data);
 		_model.tree_nodes[data].handle = _ui.ui_insert_item(_model.tree_nodes[data].text, bmap, h, nullptr);
-		_model.tree_nodes[data].flags = EDITABLE;
+		set_node_flags(data, EDITABLE);
 		_ui.ui_expand_item(h);
 	}
 }
@@ -232,7 +238,7 @@ int SexpTreeActions::add_data(const char* data, int type)
 	_model.set_node(node, type, data);
 	NodeImage bmap = _model.get_data_image(node);
 	_model.tree_nodes[node].handle = _ui.ui_insert_item(data, bmap, _model.tree_nodes[node_idx].handle, nullptr);
-	_model.tree_nodes[node].flags = EDITABLE;
+	set_node_flags(node, EDITABLE);
 	if (_model.modified)
 		*_model.modified = 1;
 	return node;
@@ -252,7 +258,7 @@ int SexpTreeActions::add_variable_data(const char* data, int type)
 	int node = _model.allocate_node(node_idx);
 	_model.set_node(node, type, data);
 	_model.tree_nodes[node].handle = _ui.ui_insert_item(data, NodeImage::VARIABLE, _model.tree_nodes[node_idx].handle, nullptr);
-	_model.tree_nodes[node].flags = NOT_EDITABLE;
+	set_node_flags(node, NOT_EDITABLE);
 	if (_model.modified)
 		*_model.modified = 1;
 	return node;
@@ -275,7 +281,7 @@ int SexpTreeActions::add_container_name(const char* container_name)
 	_model.set_node(node, (SEXPT_VALID | SEXPT_CONTAINER_NAME | SEXPT_STRING), container_name);
 	_model.tree_nodes[node].handle =
 		_ui.ui_insert_item(container_name, NodeImage::CONTAINER_NAME, _model.tree_nodes[node_idx].handle, nullptr);
-	_model.tree_nodes[node].flags = NOT_EDITABLE;
+	set_node_flags(node, NOT_EDITABLE);
 	if (_model.modified)
 		*_model.modified = 1;
 	return node;
@@ -296,7 +302,7 @@ void SexpTreeActions::add_container_data(const char* container_name)
 	_model.set_node(node, (SEXPT_VALID | SEXPT_CONTAINER_DATA | SEXPT_STRING), container_name);
 	_model.tree_nodes[node].handle =
 		_ui.ui_insert_item(container_name, NodeImage::CONTAINER_DATA, _model.tree_nodes[node_idx].handle, nullptr);
-	_model.tree_nodes[node].flags = NOT_EDITABLE;
+	set_node_flags(node, NOT_EDITABLE);
 	_model.item_index = node;
 	if (_model.modified)
 		*_model.modified = 1;
@@ -322,7 +328,7 @@ void SexpTreeActions::add_operator(const char* op, void* parent_handle)
 		_model.tree_nodes[node].handle = _ui.ui_insert_item(op, NodeImage::OPERATOR, _model.tree_nodes[_model.item_index].handle, nullptr);
 	}
 
-	_model.tree_nodes[node].flags = OPERAND;
+	set_node_flags(node, OPERAND);
 	_model.item_index = node;
 	if (_model.modified)
 		*_model.modified = 1;
@@ -391,7 +397,7 @@ void SexpTreeActions::add_or_replace_operator(int op, int replace_flag)
 				if (i < 0) {
 					_model.set_node(_model.item_index, (SEXPT_OPERATOR | SEXPT_VALID), Operators[op].text.c_str());
 					_ui.ui_set_item_text(_model.tree_nodes[_model.item_index].handle, Operators[op].text.c_str());
-					_model.tree_nodes[_model.item_index].flags = OPERAND;
+					set_node_flags(_model.item_index, OPERAND);
 					return;
 				}
 			}
@@ -498,7 +504,6 @@ int SexpTreeActions::insert_operator(int op, void* root_parent_handle)
 
 	const int node = _model.allocate_node(parent_node, wrapped_node);
 	_model.set_node(node, (SEXPT_OPERATOR | SEXPT_VALID), Operators[op].text.c_str());
-	_model.tree_nodes[node].flags = node_flags;
 
 	void* parent_handle = nullptr;
 	if (parent_node >= 0) {
@@ -521,6 +526,7 @@ int SexpTreeActions::insert_operator(int op, void* root_parent_handle)
 	}
 
 	_model.tree_nodes[node].handle = _ui.ui_insert_item(Operators[op].text.c_str(), NodeImage::OPERATOR, parent_handle, wrapped_handle);
+	set_node_flags(node, node_flags);
 
 	_ui.ui_move_branch(wrapped_node, node);
 	_model.item_index = node;
diff --git a/code/missioneditor/sexp_tree_actions.h b/code/missioneditor/sexp_tree_actions.h
index 24109550617..5d5914bea48 100644
--- a/code/missioneditor/sexp_tree_actions.h
+++ b/code/missioneditor/sexp_tree_actions.h
@@ -125,6 +125,9 @@ class SexpTreeActions {
 	bool rename_container_nodes(const SCP_string& old_name, const SCP_string& new_name);
 
 private:
+	// Update model flags and synchronize the widget's inline editability.
+	void set_node_flags(int node_index, int flags);
+
 	// Delete all UI children of a node and free their model data.
 	// Resets the model's child link to -1.
 	void clear_node_children(int node_index);
diff --git a/code/missioneditor/sexp_tree_model.h b/code/missioneditor/sexp_tree_model.h
index 61b171e09f5..1a2fb7b8003 100644
--- a/code/missioneditor/sexp_tree_model.h
+++ b/code/missioneditor/sexp_tree_model.h
@@ -248,6 +248,8 @@ class ISexpTreeUI {
 	virtual void ui_set_item_text(void* handle, const char* text) = 0;
 	// Update the icon of a tree item
 	virtual void ui_set_item_image(void* handle, NodeImage image) = 0;
+	// Sync native widget editability. FRED2 checks the model flags when editing instead.
+	virtual void ui_set_item_editable(void* /*handle*/, bool /*editable*/) {}
 	// Return the first child handle of the given tree item, or nullptr if none
 	virtual void* ui_get_child_item(void* handle) const = 0;
 	// Return true if the tree item has any children
diff --git a/qtfred/src/mission/dialogs/ShipEditor/ShipEditorDialogModel.cpp b/qtfred/src/mission/dialogs/ShipEditor/ShipEditorDialogModel.cpp
index dd8cfa18bcf..a0765e8ff5d 100644
--- a/qtfred/src/mission/dialogs/ShipEditor/ShipEditorDialogModel.cpp
+++ b/qtfred/src/mission/dialogs/ShipEditor/ShipEditorDialogModel.cpp
@@ -14,6 +14,7 @@
 #include "mission/missionmessage.h"
 #include "mission/missionparse.h"
 #include "missioneditor/common.h"
+#include "missioneditor/sexp_tree_model.h"
 
 #include <globalincs/linklist.h>
 #include <globalincs/utility.h>
@@ -1332,12 +1333,11 @@ bool ShipEditorDialogModel::getArrivalCue() const
 	return _updateArrival;
 }
 
-void ShipEditorDialogModel::setArrivalTreeDirty(int formula)
+void ShipEditorDialogModel::setArrivalTreeDirty(const SexpTreeModel& tree)
 {
 	if (_multiEdit && !_updateArrival)
 		return;
 
-	_arrivalTreeFormula = formula;
 	_updateArrival = true;
 
 	for (auto* ptr = GET_FIRST(&obj_used_list); ptr != END_OF_LIST(&obj_used_list); ptr = GET_NEXT(ptr)) {
@@ -1345,9 +1345,11 @@ void ShipEditorDialogModel::setArrivalTreeDirty(int formula)
 			auto i = ptr->instance;
 			if (Ships[i].wingnum >= 0)
 				continue;
-			if (Ships[i].arrival_cue >= 0 && Ships[i].arrival_cue != formula)
+			if (Ships[i].arrival_cue >= 0)
 				free_sexp2(Ships[i].arrival_cue);
-			Ships[i].arrival_cue = formula;
+			// Each ship owns its cue, so serialize a separate expression for each one.
+			Ships[i].arrival_cue = tree.save_tree();
+			_arrivalTreeFormula = Ships[i].arrival_cue;
 		}
 	}
 
@@ -1494,12 +1496,11 @@ bool ShipEditorDialogModel::getDepartureCue() const
 	return _updateDeparture;
 }
 
-void ShipEditorDialogModel::setDepartureTreeDirty(int formula)
+void ShipEditorDialogModel::setDepartureTreeDirty(const SexpTreeModel& tree)
 {
 	if (_multiEdit && !_updateDeparture)
 		return;
 
-	_departureTreeFormula = formula;
 	_updateDeparture = true;
 
 	for (auto* ptr = GET_FIRST(&obj_used_list); ptr != END_OF_LIST(&obj_used_list); ptr = GET_NEXT(ptr)) {
@@ -1507,9 +1508,11 @@ void ShipEditorDialogModel::setDepartureTreeDirty(int formula)
 			auto i = ptr->instance;
 			if (Ships[i].wingnum >= 0)
 				continue;
-			if (Ships[i].departure_cue >= 0 && Ships[i].departure_cue != formula)
+			if (Ships[i].departure_cue >= 0)
 				free_sexp2(Ships[i].departure_cue);
-			Ships[i].departure_cue = formula;
+			// Each ship owns its cue, so serialize a separate expression for each one.
+			Ships[i].departure_cue = tree.save_tree();
+			_departureTreeFormula = Ships[i].departure_cue;
 		}
 	}
 
diff --git a/qtfred/src/mission/dialogs/ShipEditor/ShipEditorDialogModel.h b/qtfred/src/mission/dialogs/ShipEditor/ShipEditorDialogModel.h
index 550ec24e958..b69ab2034d1 100644
--- a/qtfred/src/mission/dialogs/ShipEditor/ShipEditorDialogModel.h
+++ b/qtfred/src/mission/dialogs/ShipEditor/ShipEditorDialogModel.h
@@ -4,6 +4,8 @@
 #include "mission/util.h"
 #include "ship/ship.h"
 
+class SexpTreeModel;
+
 namespace fso::fred::dialogs {
 
 class ShipEditorDialogModel : public AbstractDialogModel {
@@ -84,7 +86,7 @@ class ShipEditorDialogModel : public AbstractDialogModel {
 	void setArrivalCue(bool updateCue);
 	bool getArrivalCue() const;
 
-	void setArrivalTreeDirty(int formula);
+	void setArrivalTreeDirty(const SexpTreeModel& tree);
 	int getArrivalFormula() const;
 
 	void setNoArrivalWarp(int state);
@@ -107,7 +109,7 @@ class ShipEditorDialogModel : public AbstractDialogModel {
 	void setDepartureCue(bool updateCue);
 	bool getDepartureCue() const;
 
-	void setDepartureTreeDirty(int formula);
+	void setDepartureTreeDirty(const SexpTreeModel& tree);
 	int getDepartureFormula() const;
 	void setNoDepartureWarp(int state);
 	int getNoDepartureWarp() const;
diff --git a/qtfred/src/ui/dialogs/ShipEditor/ShipEditorDialog.cpp b/qtfred/src/ui/dialogs/ShipEditor/ShipEditorDialog.cpp
index c52bbc03da1..0f649313f4c 100644
--- a/qtfred/src/ui/dialogs/ShipEditor/ShipEditorDialog.cpp
+++ b/qtfred/src/ui/dialogs/ShipEditor/ShipEditorDialog.cpp
@@ -862,7 +862,7 @@ void ShipEditorDialog::on_noArrivalWarpCheckBox_stateChanged(int state)
 }
 void ShipEditorDialog::on_arrivalTree_modified()
 {
-	_model->setArrivalTreeDirty(ui->arrivalTree->_model.save_tree());
+	_model->setArrivalTreeDirty(ui->arrivalTree->_model);
 }
 void ShipEditorDialog::on_arrivalTree_helpChanged(const QString& help)
 {
@@ -898,7 +898,7 @@ void ShipEditorDialog::on_updateDepartureCueCheckBox_toggled(bool value)
 }
 void fred::dialogs::ShipEditorDialog::on_departureTree_modified()
 {
-	_model->setDepartureTreeDirty(ui->departureTree->_model.save_tree());
+	_model->setDepartureTreeDirty(ui->departureTree->_model);
 }
 void ShipEditorDialog::on_departureTree_helpChanged(const QString& help)
 {
diff --git a/qtfred/src/ui/widgets/sexp_tree_view.cpp b/qtfred/src/ui/widgets/sexp_tree_view.cpp
index 2da22b6355e..ac0205157a4 100644
--- a/qtfred/src/ui/widgets/sexp_tree_view.cpp
+++ b/qtfred/src/ui/widgets/sexp_tree_view.cpp
@@ -312,6 +312,13 @@ void sexp_tree_view::ui_set_item_image(void* handle, NodeImage image)
 	applyNodeIcon(static_cast<QTreeWidgetItem*>(handle), image);
 }
 
+// Keep Qt inline editing consistent with the shared model after node type changes.
+void sexp_tree_view::ui_set_item_editable(void* handle, bool editable)
+{
+	auto* item = static_cast<QTreeWidgetItem*>(handle);
+	item->setFlags(item->flags().setFlag(Qt::ItemIsEditable, editable));
+}
+
 // Returns the first child QTreeWidgetItem, or nullptr. Called by _actions to traverse the tree.
 void* sexp_tree_view::ui_get_child_item(void* handle) const
 {
@@ -587,6 +594,7 @@ QTreeWidgetItem* sexp_tree_view::move_branch(QTreeWidgetItem* source, QTreeWidge
 	// Create the destination item
 	const auto icon = source->icon(0);
 	QTreeWidgetItem* h = insertWithIcon(source->text(0), icon, parent, after);
+	h->setFlags(source->flags());
 	if (idx < tree_nodes.size()) {
 		tree_nodes[idx].handle = h;
 	}
@@ -630,6 +638,7 @@ void sexp_tree_view::copy_branch(QTreeWidgetItem* source, QTreeWidgetItem* paren
 
 	const auto icon = source->icon(0);
 	QTreeWidgetItem* h = insertWithIcon(source->text(0), icon, parent, after);
+	h->setFlags(source->flags());
 	size_t idx = 0;
 	for (; idx < tree_nodes.size(); ++idx) {
 		if (tree_nodes[idx].handle == source) {
@@ -1815,9 +1824,10 @@ void sexp_tree_view::insertOperatorAction(int op) {
 	auto* old_item = tree_item_handle(tree_nodes[item_index]);
 	auto* root_parent = old_item ? old_item->parent() : nullptr;
 	const int old_item_index = item_index;
+	const bool is_formula_root = tree_nodes[old_item_index].parent == -1;
 	const int node = _actions.insert_operator(op, root_parent);
 
-	if (_interface->getFlags()[TreeFlags::LabeledRoot] && root_parent != nullptr) {
+	if (is_formula_root && _interface->getFlags()[TreeFlags::LabeledRoot] && root_parent != nullptr) {
 		rootNodeFormulaChanged(old_item_index, node);
 		root_parent->setData(0, FormulaDataRole, node);
 	}
@@ -1882,6 +1892,10 @@ void sexp_tree_view::replaceStringDataHandler() {
 // Sets the _currently_editing flag and calls Qt's editItem() to start inline text editing.
 // The flag ensures that handleItemChange() only processes intentional edits, not programmatic changes.
 void sexp_tree_view::beginItemEdit(QTreeWidgetItem* item) {
+	if (item == nullptr || !item->flags().testFlag(Qt::ItemIsEditable)) {
+		return;
+	}
+
 	_currently_editing = true;
 	
 	editItem(item);
diff --git a/qtfred/src/ui/widgets/sexp_tree_view.h b/qtfred/src/ui/widgets/sexp_tree_view.h
index a72c3692965..9e163d048d7 100644
--- a/qtfred/src/ui/widgets/sexp_tree_view.h
+++ b/qtfred/src/ui/widgets/sexp_tree_view.h
@@ -195,6 +195,7 @@ class sexp_tree_view: public QTreeWidget, public ISexpTreeUI {
 	void ui_delete_item(void* handle) override;                  //!< Deletes a QTreeWidgetItem
 	void ui_set_item_text(void* handle, const char* text) override;   //!< Sets display text via setText()
 	void ui_set_item_image(void* handle, NodeImage image) override;   //!< Sets icon via setIcon()
+	void ui_set_item_editable(void* handle, bool editable) override; //!< Syncs Qt::ItemIsEditable with model flags
 	void* ui_get_child_item(void* handle) const override;        //!< Returns first child item, or nullptr
 	bool ui_has_children(void* handle) const override;           //!< Returns true if childCount() > 0
 	void ui_expand_item(void* handle) override;                  //!< Expands a single item via setExpanded()