diff --git a/CHANGELOG.md b/CHANGELOG.md
index 1a4115ecc..59b2cd292 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -8,6 +8,7 @@ This is a work-in-progress for the next QuPath release.
 * `isOverlayNG` should be turned on by default (https://github.com/qupath/qupath/issues/1244)
 * Labeled image instance export doesn't work as expected for z-stacks (https://github.com/qupath/qupath/issues/1267)
 * Fix PathClass singleton creation when a derived PathClass is requested (https://github.com/qupath/qupath/pull/1286)
+* 'Run for project' does not recognize when previous images have been deleted (https://github.com/qupath/qupath/issues/1291)
 
 ### Dependency updates
 * Bio-Formats 7.0.0
diff --git a/qupath-gui-fx/src/main/java/qupath/lib/gui/scripting/DefaultScriptEditor.java b/qupath-gui-fx/src/main/java/qupath/lib/gui/scripting/DefaultScriptEditor.java
index f74238afd..3ea81b1be 100644
--- a/qupath-gui-fx/src/main/java/qupath/lib/gui/scripting/DefaultScriptEditor.java
+++ b/qupath-gui-fx/src/main/java/qupath/lib/gui/scripting/DefaultScriptEditor.java
@@ -446,7 +446,8 @@ private void initializeActions() {
 		beautifySourceAction.setAccelerator(new KeyCodeCombination(KeyCode.L, KeyCombination.SHORTCUT_DOWN, KeyCombination.ALT_DOWN));
 		beautifySourceAction.disabledProperty().bind(canBeautifyBinding);
 		compressSourceAction.disabledProperty().bind(canCompressBinding);
-		
+
+		// Reset previous images when the project changes
 		qupath.projectProperty().addListener((v, o, n) -> {
 			previousImages.clear();
 		});
@@ -1535,7 +1536,11 @@ void handleRunProject(final boolean doSave) {
 //		FilteredList<ProjectImageEntry<?>> sourceList = new FilteredList<>(FXCollections.observableArrayList(project.getImageList()));
 		
 		String sameImageWarning = "A selected image is open in the viewer!\nAny unsaved changes will be ignored.";
-		var listSelectionView = ProjectDialogs.createImageChoicePane(qupath, project.getImageList(), previousImages, sameImageWarning);
+		var imageList = project.getImageList();
+		// Remove any images that have been removed from the project
+		// See https://github.com/qupath/qupath/issues/1291
+		previousImages.retainAll(new HashSet<>(imageList));
+		var listSelectionView = ProjectDialogs.createImageChoicePane(qupath, imageList, previousImages, sameImageWarning);
 		
 		Dialog<ButtonType> dialog = new Dialog<>();
 		dialog.initOwner(qupath.getStage());