Right now there are some synchronisation problems if using identical caches within 2 different folders.
I've described the troubles and ideas to solve them here:
http://help.locusmap.eu/topic/geocaching-identical-caches-within-different-folders (http://help.locusmap.eu/topic/geocaching-identical-caches-within-different-folders)
Great idea. But it should not compare between only 2 folders as I work with many more for different locations I'm visiting regularly.