I know it's not necessarily a chore to do a manual clean, but I found the time to write a quick program to do it for you. Put this file in BF2_ModTools folder. It will prompt for the 3 letter map name when run, and all that'll be left is to delete the map from the addon folder.

Right now, I don't have a map to test this on since my modtools are acting up, so I just created files to do the testing. Be that as it may, I think it's ready, though I would appreciate if a few people would run it just to make sure.

ManualClean.exe - unfixed

Frisbeeterrian it wont work it says that it has wrong configuration or something.

There was a possibility of something like that happening, let me fix it.

Edit: It helps to post a release version and not a debug version, sorry. Fixed in first post.