Lost databases - linked to Mountain Lion upgrade?

I have DEVONThink Pro Office (version 2.3.5) installed on my Mac. Immediately after I upgraded to Mountain Lion (last weekend), 3 out of the 8 databases in my Devonthink application disappeared from my system and I cannot find any trace of any of them on my hard drive or any of the substantial amount of data stored within them. Like the 5 databases that are still accessible, the 3 missing databases were saved in my ~/Documents folder. The only ‘remnants’ of these databases are to be found:

(i) in the Devonthink sorter, which still shows the inboxes of 2 of the databases which I had previously set up; and
(ii) when I access Exposé when in Devonthink (i.e. to see minatures of each open Devonthink window), the row of little icons at the bottom of the screen shows icons for all 8 databases, including the missing 3, but clicking on any one of the missing 3 database icons only takes me back to the main Devonthink window.

I accessed 2 of these missing databases only a week ago (before my Mountain Lion upgrade) without issue. I regularly back up my computer using Time Machine and (mysteriously) cannot find any reference to any of these missing databases or the data that is stored within them when looking through ~/Documents folder and elsewhere during the last few months in Time Machine. I am certain that I have not erroneously deleted these databases in the last few days (and even if I had, should they not appear in Time Machine when viewing earlier back-ups?).

I would be grateful for any thoughts or suggestions as to what might have caused this issue. Has anyone else had any similar problems; perhaps arising after upgrading to Mountain Lion? Many thanks in advance for any assistance.

Wait, you still haven’t gotten a reply on this?

Please tell me that someone from DevonTech contacted you about this. This is serious.

This is a mystery. After installing ML you find that some files are missing. And now, you find the files are not even in time machine backups. Have you been over to Apple’s OSX Mountain Lion forum and posted there, or looked through recent posts. I don’t see where this is a DT issue as much as an OSX install issue. However, the missing backups in time machine …

I upgraded to Mountain Lion (2.3.5 Devonthink Office Pro) and experienced the following

  1. All the metadata in all my databases were lost
  2. None of the backups were recognised
  3. Rebuilding and Verifying the database [Tools] created all orphan files

The metadata for the files still exists (separate folder) but not in a way Devonthink Office Pro (2.3.5) could recognize.

I have just been alerted that a Devonthink Office Pro upgrade has been released which has been stated to be made compatible with Mountain Lion. I am hopeful the databases can be rebuilt without loss of (too much) metadata.

I will keep you posted.

Unable to Rebuild the Databases.

I now have over 1000 orphaned files.