Oh dear. (Odd that the number is so precise as “31000”.)
Yes, I can imagine that lack of disk space is going to lead to issues…
Are the files indexed or imported? If indexed, are those files still in the macOS file system?
Do you have a backup from which you can restore? TimeMachine? DEVONthink Database Archive?
So as to not repeat DEVONthink’s advice, see “REPAIRING A DEFECTIVE DATABASE”, page 192 of 3.9.6 version of the DEVONManual, or in Help for a starting point.