I had fresh installed a 'nix desktop, and Lc 9.0.1 to answer a question here on the forums. I opened a project that was created in Lc 6.5.2, which is started by a basic 'launcher' standalone that was compiled in 6.5.2.
I then copied some code, and closed the IDE. I didn't modify anything in the stack, and clicked on 'Don't Save' in the dialog when I closed the IDE.
I later finished setting up the 'nix install, and started experiencing issues with the program I had opened in 9.x starting where it had been running fine on this fresh install before opening in 9.x.
I then tried to open it in Lc 6.5.2 to see if there was an issue with the code I had previously missed somehow. Imagine my surprise when 6.5.2 could not open this stack (file is not a stack error), but 8.x and 9 opened it with no issue.
I then opened it in 8.x and 9.x and clicked on save as. I have the preferences set to save legacy stacks back as the format they were written in, and it correctly identified the legacy format as 5.5. I saved it as that overwriting the file, and then tried to open it in 6.5.2, and it failed to open it again

To me, it looks like just opening a file in 9.x somehow changed the format of the file in such a way that it could no longer be read by the version it was created in.
I always have redundant copies of my projects around, so it didn't cost me any more time than restoring the backup (which again worked fine and was open-able in 6.5.x), but I think it is odd enough to investigate or at least mention here, because I am quite sure this would not be the expected behavior.
If someone else has input on this, I'd sure like to hear it. If no one else does, I'll be submitting a bug report later.