How are you checking if the maps are there? If they are removed from the lists it is impossible for them to appear in the rotation votes. However if the maps are still saved on the server they will show up when you enter commands into console asking for map lists. Rcon bypasses the lists of "allowed" maps and grants access to everything. For example from hlsw I can force the server to maps not on the list if they are on the server. But when they are "removed" they can not show up in votes and so effectively they are not really there.