A big part of our confusion is that you're asking about files in the Finder without providing us the connection to FCPX or why you think FCPX is the culprit other than these green icons seem to have started to appear after you updated FCPX. but now you have indicated that you also performed an OS update and a pro format update.
Tom's ability to see through the details is better an most of ours but here's what I'd need to know:
1. Original footage came from what camera and in what format?
2. Do you still have the original footage available?
3. What format were you editing in? The files you are looking at in the Finder are your exports or shared files, correct?
4. What format did you export to and why (as Tom says, weird frame size for h.264)?
5. What is your worst case recovery scenario? Do you have the original footage, do you have backups of your libraries. etc.
6. You may have copied those output files to another server for approvals, you may have a backup of them. Do they exhibit the same issues?
7. You said you are continuing to work. I'd suggest you stop using H.264 until you solve this. Assemble your projects using ProRes422 and share the project as a 422 movie. Then use Compressor to create your H.264 AFTER you've solved this problem.
If you have not been creating a backup from which you can recover the entire project (a "black start" backup that you could just take to another Mac with FCPX installed and and get back to work), do so before you get to much further along.
I hope Tom has better and simpler guidance for you.