Indexed database of OneDrive folder has a missing reference... and won't reindex

Check this thread on recent changes to OneDrive; there are other threads linked from there. As you are only seeing one file affected, I am guessing that this is not going to be the issue - but I am not sure. In any case it may be worth changing the absolute paths in DEVONthink if you have not yet done so. If you do make such a change, it is essential it should be made (at the same time) on every installation of DEVONthink, insofar as they are synced. That also requires that the OneDrive client is identical on all devices.