diff --git a/src/lib/data/SqliteStorage.cpp b/src/lib/data/SqliteStorage.cpp
index e415f068..ba63fe46 100644
--- a/src/lib/data/SqliteStorage.cpp
+++ b/src/lib/data/SqliteStorage.cpp
@@ -160,6 +160,14 @@ void SqliteStorage::removeNameHierarchyElement(Id id)
 	).c_str());
 }
 
+void SqliteStorage::removeElementsWithLocationInFiles(const std::vector<Id>& fileIds)
+{
+	m_database.execDML((
+		"DELETE FROM element WHERE id IN (SELECT element_id FROM source_location "
+			"WHERE source_location.file_node_id IN (" + utility::join(utility::toStrings(fileIds), ',') + "));"
+	).c_str());
+}
+
 void SqliteStorage::removeFile(Id id)
 {
 	if (isFile(id))
diff --git a/src/lib/data/SqliteStorage.h b/src/lib/data/SqliteStorage.h
index 48e3ac12..8c412fc4 100644
--- a/src/lib/data/SqliteStorage.h
+++ b/src/lib/data/SqliteStorage.h
@@ -40,6 +40,7 @@ public:
 
 	void removeElement(Id id);
 	void removeNameHierarchyElement(Id id);
+	void removeElementsWithLocationInFiles(const std::vector<Id>& fileIds);
 	void removeFile(Id id);
 	void removeFiles(const std::vector<Id>& fileIds);
 	void removeUnusedNameHierarchyElements();
diff --git a/src/lib/data/Storage.cpp b/src/lib/data/Storage.cpp
index 78247c2d..d56c1d04 100644
--- a/src/lib/data/Storage.cpp
+++ b/src/lib/data/Storage.cpp
@@ -87,6 +87,7 @@ void Storage::clearFileElements(const std::vector<FilePath>& filePaths)
 
 	if (fileNodeIds.size())
 	{
+		m_sqliteStorage.removeElementsWithLocationInFiles(fileNodeIds);
 		m_sqliteStorage.removeFiles(fileNodeIds);
 	}
 }