Yesterday I had just this issue in two of my databases in all my iThings. I think it was caused because I reinstalled macOS and instead of regenerate a new Global Inbox, I restored databases and the entire Devonthink 3 folder in Application Support.
I solved following cgrunenberg procedure, but only for the offending databases, not the entire sync database. One was shared between iThings and aThings, but the other was only between macOS only. None indexed.