Ah, so you mean you were recompiling a module SWF and reloading it, while the other half was still in debugger? I'm not sure, but I think that the policy as to load and unload is per domain... but, that's something I really don't know. Is it possible that after unloading a SWF only some class definitions would "stuck" in the player? Sounds fishy :)
In other aspects, I didn't mean "no version at all", I'm for "per SWF", so if the entire SWF was cached, then you would discover it by looking at the version in SWF.