If everything else fails, there's a rather time-consuming method for
identifying broken game mods that may work.
Here's a method that should work for Calibre:
1. Backup your library first. Then create two new temporary libraries, Test 1 and Test 2.
2. Use Calibre's "copy to library" (
don't use delete after copy!) to copy half of your books to Test 1 and other half to Test 2.
3. Let the FTS indexer run on each of the libraries, one at a time.
4. When you identify which one has stalled, use 'copy to library' (you can safely use 'delete after copy' now) split the books into two more test libraries and repeat #3.
Then just keep repeating 3 and 4 until you figure out which file it is.