I moved some symbol from one library to another, and correspondingly replaced the symbol in my schematic. When I now open the Footprint Association, the window is greyed out (probably caused by KDE), doesn’t show any mappings, and the window is unresponsive. I cannot even close the window, but have to kill Kicad.
And there have been quite some bug fixes after that.
So the first thing to do is to make a backup to prevent any escalation and then update to the latest stable (V5.1.8).
If that does not work, then revert to the backup you (probably didn’t) make just before you did your thing with the library.
If that does not work, you can open the file in a text editor and remove the offending part from it manually.
Please do make notes and report back your results. If this is related to a bug in the current KiCad release, the developers are very keen on any info that can help them in finding the cause of the bug.
You probably did: Eeschema / Tools / Assign Footprints (Or clicked on the corresponding Icon in Eeschema). This does not use separate files, but communicates directly with Eeschema itself.
In KiCad V5.1.x the schematic symbols itself is not even in the schematic (V5.99 has copies of the schematic symbols embedded in the file), but it is just a link to an external library. If the link is broken then you see the [??] placeholders for schematic symbols.
From the info I have, the problem is probably with the schematic symbol in the library itself, or possibly with the [project]-cache.lib. You can try to delete the [project]-cache.lib, as normally KiCad can re-create this file as long as the original libraries are still visible. (You do have backups now right?)
If you’re willing to share your project, you can zip the whole project and upload it here, and I’ll have a look at it to see if I can fix it.