This is just going to be a quick post as I am under the pump at work at the moment (which is a good thing, right?)
Recently I upgraded to Flash Pro CS5 and came across an issue which upon opening a file recently saved as a CS5 .FLA or .XFL, it would fail to open and output an error "Flash can not parse this document."
Thankfully, I had version control enabled and I managed to rescue a day old version of the swf I had been working on. Upon flagging the issue with Adobe and getting a response from them, it appears that they have narrowed down the cause of the issue.
Basically if you have a movieclip in your library that contains a layer with NO KEYFRAMES (see image below), and you save the file in a CS5 format - then you will now have a corrupted file that you won't be able to open.
So how to avoid this? There are two things that I would do...
1) Backup and backup often. I set up my Windows 7 machine to automatically backup my working projects each afternoon to a designated folder on the network. Version control and incremental archiving saved my ass this time around, but in the past I have not been so lucky. Avoid heartache - do it... NOW!!!
2) Do not leave any empty layers within any movieclips in your library. If you do, and you save, you will have a useless file.
Until Adobe come out with a patch for this issue (which they should now that we have flagged it with them and their techs have identified the cause) heed my word people!