This is most definitely an area where Adobe needs to apply some resources. (I've had my local subversion repository hosed twice by Flex Builder. They don't like to get along. In part because the default behavior of FB is to import tons of stuff to the bin folder. Which causes chaos as it also moves .svn folders.)
I'm going to try to utilize Subclipse. And restructure my directory layout. That said one key to the problem is turning off the import to bin of non-embedded files. See #9 http://thesaj.wordpress.com/2007/11/06/flex-builder-tips-tricks/
