I have a Flash project, and it has many source files. I have a fairly heavily-used class, call it Jenine. I recently (and, perhaps, callously) relocated Jenine from one name
I have found one related behaviour that may help (sounds like your specific problem runs deeper though):
Flash checks whether a source file needs recompiling by looking at timestamps. If its compiled version is older than the source file, it will recompile. But it doesn't check whether the compiled version was generated from the same source file or not.
Specifically, if you have your actionscript files under version control, and you Revert a change, the reverted file will usually have an older timestamp, and Flash will ignore it.