Create a brand new file with just one new table. Test and see if the Unique values setting is retained for it when you make this selection. If it works like you expect, then your other file may be damaged. You can check your file for damage and usually repair it using FileMaker's Recover option from the File menu.
Things to keep in mind about Recover:
While Recover almost always detects and fully corrects any problems with your file...
- The recovered copy may behave differently even if recover reports "no problems found".
- Recover does not detect all problems
- Recover doesn't always fix all problems correctly
- Best Practice is to never put a recovered copy back into regular use or development. Instead, replace the damaged file with an undamaged back up copy if this is at all possible. You may have to save a clone of the back up copy and import all data from your recovered copy to get a working copy with the most up to date information possible.
And here's a knowledgebase article that you may find useful: What to do when your file is corrupt (KB5421).
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