I've been having very much the same problem. I create a new Flash file from scratch, import a few assets from Illustrator CC, and just write some Actionscript for basic movement and interactivity. It can work fine this way for several hours. But if I save and come back to the file the later that day or the next morning, I get this error and the timeline and library are completely empty.
Can you please check your PublishSettings.xml file whether is there any duplicate profile entries?
You can check the same by renaming your .fla to .zip and extract the zip file to open the PublishSettings.xml
If you find multiple duplicate profile entries then please remove all the duplicate entries from the file and rename the file back to .fla and see if that helps.