@redx Yes, it would cause issues as players get maps & mods they don't have from the FAF servers, not from other players. The only way to get around that with manually renaming the folder is to use file sharing to send or allow access to the renamed folder to other players. This is not ideal & some may not want to deal with that.
The proper way to handle mapgen maps is as stated earlier; copy/paste the map name someplace safe & then copy/paste that into the Map Name field of generator when you want to play that map again. The other method would be the folder copy/paste procedure stated earlier.
There is of course the method that magge pointed out regarding amending the generator code, but I don't know if that's a long term solution as that could be overridden by client updates.