Yes, if there are errors in your database, from whatever cause, it’s time to undertake maintenance, as continuing to use the database with errors may cause still more errors.
Quit your DEVONthink application. In the Finder, make a zipped copy of the database and reserve it for possible future references. NOTE: Never make a Finder copy of an open database, as the copy may be incomplete or contain errors.
Relaunch DEVONthink. Choose Tools > Rebuild Database. When the Rebuild operation is complete, examine the Log (Window > Log) to see if there are files that are listed as having failed to be included. If so, save the Log list as you will probably want to try to find and re-import those files. (Perhaps they are recoverable from the copy of the database you had made, in Files.noindex within the database.)
Select Tools > Verify & Repair. If there are no errors, you have recovered a sound working database. I would recommend frequent external backups, such as via Time Machine and/or (for DT Pro/Office) the Backup Archive procedure (Scripts > Export > Backup Archive).
Now it’s time to worry about what may have caused problems. If you haven’t done so regularly, run a suite of OS X maintenance operations using a utility such as C ocktail or OnyX, including cleaning out caches. Run Apples Disk Utility check disk routine to see if there are problems with your disk directory.
Have you recently installed some new software, perhaps a utility that modifies the appearance or behavior of OS X in some way? Think about any third-party preference panes, or software that has installed an Input Manager plugin, a QuickTime plugin or a Safari add-on. Try removing such software at least temporarily. Monitor your computer’s operations and check your DEVONthink database regularly using the Verify & Repair routine.
Make certain that you are not running out of hard drive space. Apple engineers recommend keeping at least 15-20% of the nominal HD space free, to accommodate OS X needs and application needs for temporary and swap files. If OS X runs out of free HD space, it may start overwriting data, with obviously data-threatening results.
Are you having problems with electricity brownouts or outages? That can result in data damage if power fluctuates while data is being written to disk, unless you have an uninterruptible power supply (or use a laptop).
What would happen to your data were your hard drive to fail? It’s a good idea to keep external backups of your important data, using Backup Archive, Time Machine or one of the good backup applications.