diff --git a/platform/external-system-api/src/com/intellij/openapi/externalSystem/settings/AbstractExternalSystemSettings.java b/platform/external-system-api/src/com/intellij/openapi/externalSystem/settings/AbstractExternalSystemSettings.java
index 71255e518dfb..2d0411a9e666 100644
--- a/platform/external-system-api/src/com/intellij/openapi/externalSystem/settings/AbstractExternalSystemSettings.java
+++ b/platform/external-system-api/src/com/intellij/openapi/externalSystem/settings/AbstractExternalSystemSettings.java
@@ -166,6 +166,9 @@ public abstract class AbstractExternalSystemSettings<
           }
           getPublisher().onUseAutoImportChange(current.isUseAutoImport(), current.getExternalProjectPath());
         }
+        if (old.isCreateEmptyContentRootDirectories() != current.isCreateEmptyContentRootDirectories()) {
+          ExternalProjectsManager.getInstance(getProject()).getExternalProjectsWatcher().markDirty(current.getExternalProjectPath());
+        }
         checkSettings(old, current);
       }
     }