In the event that you have attempted to remove a custom OEM layer from the VAM prior to removing any existing application layers that are based upon it, the message dialog shown in the following image will open.

VTS cannot allow the deletion of a custom OEM layer until the application layers that are based upon it have first been deleted. The warning message will display the name of the application layer(s) that are based on the custom OEM layer you are attempting to remove so that you may locate and delete them.