diff --git a/idea/idea-core/src/org/jetbrains/kotlin/idea/core/script/dependencies/KotlinScriptDependenciesIndexableSetContributor.kt b/idea/idea-core/src/org/jetbrains/kotlin/idea/core/script/dependencies/KotlinScriptDependenciesIndexableSetContributor.kt
index 8ef0204978e..4027a8fb39f 100644
--- a/idea/idea-core/src/org/jetbrains/kotlin/idea/core/script/dependencies/KotlinScriptDependenciesIndexableSetContributor.kt
+++ b/idea/idea-core/src/org/jetbrains/kotlin/idea/core/script/dependencies/KotlinScriptDependenciesIndexableSetContributor.kt
@@ -25,7 +25,7 @@ class KotlinScriptDependenciesIndexableSetContributor : IndexableSetContributor(
 
     override fun getAdditionalProjectRootsToIndex(project: Project): Set<VirtualFile> {
         val manager = ScriptDependenciesManager.getInstance(project)
-        return (manager.getAllScriptsClasspath() + manager.getAllLibrarySources()).toSet()
+        return (manager.getAllScriptsClasspath() + manager.getAllLibrarySources()).filterTo(LinkedHashSet()) { it.isValid }
     }
 
     override fun getAdditionalRootsToIndex(): Set<VirtualFile> = emptySet()