diff --git a/Ghidra/Framework/FileSystem/src/main/java/ghidra/framework/store/local/IndexedLocalFileSystem.java b/Ghidra/Framework/FileSystem/src/main/java/ghidra/framework/store/local/IndexedLocalFileSystem.java
index 23017290fd..056d4a63b8 100644
--- a/Ghidra/Framework/FileSystem/src/main/java/ghidra/framework/store/local/IndexedLocalFileSystem.java
+++ b/Ghidra/Framework/FileSystem/src/main/java/ghidra/framework/store/local/IndexedLocalFileSystem.java
@@ -590,6 +590,27 @@ public class IndexedLocalFileSystem extends LocalFileSystem {
 
 		indexJournal.open();
 		try {
+			String conflictedItemStorageName = findItemStorageName(parentPath, name);
+
+			String storageName = pfile.getStorageName();
+
+			if (conflictedItemStorageName != null) {
+				try {
+					if (storageName.compareTo(conflictedItemStorageName) <= 0) {
+						conflictedItemStorageName = storageName;
+						return true; // skip conflict orphan
+					}
+
+					// remove conflict orphan from index and, add newer item below
+					deallocateItemStorage(parentPath, name);
+				}
+				finally {
+					Msg.warn(this,
+						"Detected orphaned project file " + conflictedItemStorageName + ": " +
+						getPath(parentPath, name));
+				}
+			}
+
 			Folder folder = addFolderToIndexIfMissing(parentPath);
 			Item item = new Item(folder, name, pfile.getStorageName());
 			bumpNextFileIndexID(item.getStorageName());
@@ -753,6 +774,26 @@ public class IndexedLocalFileSystem extends LocalFileSystem {
 		return folder;
 	}
 
+	/**
+	 * Find an existing storage location name
+	 * @param folderPath
+	 * @param itemName
+	 * @return storage location name or null if one not defined within index
+	 */
+	private String findItemStorageName(String folderPath, String name) {
+		try {
+			Folder folder = getFolder(folderPath, GetFolderOption.READ_ONLY);
+			Item item = folder.items.get(name);
+			if (item != null) {
+				return item.itemStorage.storageName;
+			}
+		}
+		catch (NotFoundException e) {
+			// ignore
+		}
+		return null;
+	}
+
 	/**
 	 * Find an existing storage location
 	 * @param folderPath
@@ -1060,6 +1101,11 @@ public class IndexedLocalFileSystem extends LocalFileSystem {
 				newFolder = getFolder(newFolderPath, GetFolderOption.CREATE_ALL_NOTIFY);
 			}
 
+			LocalFolderItem conflictFolderItem = getItem(newFolderPath, newName);
+			if (conflictFolderItem != null) {
+				throw new DuplicateFileException("Item already exists: " + newName);
+			}
+
 			folderItem.moveTo(item.itemStorage.dir, item.itemStorage.storageName, newFolderPath,
 				newName);
 
diff --git a/Ghidra/Framework/FileSystem/src/main/java/ghidra/framework/store/local/LocalFileSystem.java b/Ghidra/Framework/FileSystem/src/main/java/ghidra/framework/store/local/LocalFileSystem.java
index a0b3725cde..b569e2b940 100644
--- a/Ghidra/Framework/FileSystem/src/main/java/ghidra/framework/store/local/LocalFileSystem.java
+++ b/Ghidra/Framework/FileSystem/src/main/java/ghidra/framework/store/local/LocalFileSystem.java
@@ -218,10 +218,9 @@ public abstract class LocalFileSystem implements FileSystem {
 				if (item != null) {
 					item.deleteContent(null);
 				}
-				else {
-					// make sure we get item out of index
-					deallocateItemStorage(folderPath, itemName);
-				}
+
+				// make sure we get item out of index
+				deallocateItemStorage(folderPath, itemName);
 			}
 			String parentPath = folderPath + (folderPath.endsWith(SEPARATOR) ? "" : SEPARATOR);
 			for (String subfolder : getFolderNames(folderPath)) {