Had the same problem with CS4 Flash and have trained myself not to change the root folder or move the location of my current flash doc while it is open. I don't have a solution for you as I have not been able to "reopen" a past file that I have corrupted this way. Best advice is that you should remember a lot of the actions and things that you did in the past 2 days and can recreate the old file a lot quicker. I also have taken screen shots of my corrupted swf animation at certain points in the animation and used them as tracing elements in my new recreated document and this helped immensely.
This issue was a valuable lesson for me - I had a deadline and had to recreate the animation from scratch. I have never moved an active flash document since.
It seems like an odd issue as I have never had a problem moving other active documents in other Adobe software or other programs (Quark, Microsoft programs).
Don't know if Adobe people have a solution for you.
What is the full file version of Flash installed CS5 .
Are you saving your files on a Network or on local drive ?
Can you please send your fla file to FlashAuthBetaBugs@adobe.com . If you are sending the .zip file , please change the .zip extension to .zzz to avoid our spam filter system.