Are these local, physically attached mount points and local directories? Or are they mounted from elsewhere (or even, mounted from elsewhere and elsewhere is this same machine?)
And what filesystem is each of these?
You could test by making a file in the simplest of places, like in /root or /home/user, and building a new input and seeing if that works. Just make a throwaway index to send that to. If that doesn't work, let us know what new or different errors you get from that.
If it does work, move that test location around a bit and see if you can find the commonality.
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