There is one time I almost always get a “beach ball” and then a red text saying file not found.
It is when I have very unstable internet. When it comes and goes. I am traveling 300 days per year and sometimes the internet is just barely working. If it is steady slow no problem, but if it turns off and on it happens all the time.
Simple solution - just turn off WiFi and Devonthink works perfect again.
Not sure if this has anything to do with your problems - just a thought.