Yes, I'd agree that it shouldn't be a problem until you manually update the paths of the library items to the assets. Usually that's what seemed to be happening, but in this case, and with several FLA files, Flash appears to be checking those paths when it opens the files, and then if the check fails then I get the error message and I end up with some bitmaps in my library that don't have any bits in them.
The thing about Flash using absolute paths may be a red herring. It seems like the first thing it does is check paths in a relative way even though the path is not listed that way in the library item's properties. It's not very transparent, whatever it's doing. (actually, I guess I have no idea what Flash is doing under the hood.)
So, on reflection, the problem probably stems from moving a folder full of assets in relations to the FLA files using them. But still, I'm really surprised that Flash is just leaving empty bitmap items in the library when it can't find the original assets. In past experience Flash would just keep the library item as it was and the problem would only turn up if you tried to update the item.
You mentioned that you were seeing this issue in CS5.5. Can you check the version number in the about box for me? Is it showing 11.5.0 or 11.5.1? We are aware of this issue and have released an update (11.5.1) for CS5.5 to fix this. If your version is 11.5.1 and you still experience this issue, please email the complete step and or file to me at FlashAuthBetaBugs@adobe.com. Before emailing please zip your file, change .zip extension to .zzz and send me that.
Flash Pro, QE