Take and test a back up copy.
Use Advanced recover options to rebuild the file's indexes. See if the recovered copy exhibits the same behavior.
That did not cure the problem. Any other ideas?
Sorry, but I know of no reason and have seen no bug reports that would suggest why your file behaves differently in FileMaker 12 than in 11.
It has been behaving fine in FM 12 until recently when I had some kind of indexing error that corrupt 2 records (leaving them with the nasty ? in every field). I recovered, used a close, imported all the data and all was fine for 12 days. Now I have this problem. So the question is do I still have some kind of indexing problem and now its choosing to be a problem just in a different way? Will scrapping the script and starting over help?
I wish that you had told me that from the beginning. If it worked before as an FMP12 file, then something has changed since the conversion to produce this issue.
An indexing problem is what I suspected from the beginning. That why I suggested using recover to rebuild the indexes and testing the recovered copy to see if this corrected the issue.
While Recover almost always fully and correctly repairs damage to your file, it isn't perfect. If you recovered the file and have then been using the recovered copy, it's possible that the recover didn't fully repair the damage. Best practice is to replace your damaged file with an undamaged back up copy instead of using the recovered copy. If necessary, you can import the data into a clone of such a backup.
But that may be what you did when you had the original problem or did you clone the reovered file?
If you cloned a back up copy, it's not impossible that the back up copy was already damaged, but that the damaged had not become observable yet and you may need to use an older backup copy if you have it.
I'm not confident that replacing the script will fix the issue, but it might work and is probably your simplest/quickest next fix to try.
You can also try doing a "full up" recover on the file to see if the recovered file still has this issue.
Sorry, I thought I was clear about the FM12 file. I managed to get everything working again. However, I am less interested in how to fix the problem an more interested in why it's happening in the first place. Is there a way to methodically go through and find something that is triggering an indexing problem or is this simply the underlying Filemaker code that is faulty? I'd really love to avoid this mess again if possible.
I know of no diagnostic text that will report a problem with an index. Recover simply purges an index and rebuilds it from scratch when you recover a file.