Stuck on "Starting …"

Please note that SQLite does not honor the hint to use a new tempfolder from the options. You need to set the environment variable TMPDIR to change the temporary folder.

From what I can see in the code, the query you reported as taking 2 hours (wow!) is rebuilding missing index file(s). Do you have any idea why it would recreate the index file? Was it deleted? Any error messages?

No worry, it just scans the files before it finds that they are not changed. It is also discussed here:

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