For the tool Manage Map Server Cache Tiles (Server), the Update Modes available currently are:
- Recreate Empty Tiles—Only tiles that are empty will be created. Existing tiles will be left unchanged. This option is not available for web tile layers published to ArcGIS Online.
- Recreate All Tiles—Existing tiles will be replaced and new tiles will be added if the extent has changed.
- Delete Tiles—Tiles will be deleted from the cache. The cache folder structure will not be deleted.
My suggestion is that when selecting "Recreate Empty Tiles" it works instead of ignoring the selection and recreating all of the tiles anyway.
