I’ve noticed what seems to be an unusual “feature” of DEVONthink in my recent usage, and I was wondering if it is intentional. If I import an iThoughts file, it becomes a DEVONthink file, and if I view it in the Finder, the default application for opening it becomes DEVONthink. I notice that this doesn’t usually happen with other types of files that I import (e.g., Pages files are still Pages files, and their default application remains Pages). The behaviour of iThoughts files in DEVONthink is a little inconvenient and makes them slightly more difficult to open. It is no great drama, just not an ideal situation, from my point of view. But if there is a good reason for it, no worries.
Definitely weird. DEVONthink doesn’t modify imported files/folders nor does it change the default application. What’s the extension of these files before/after importing?
I don’t see this behavior. Importing an .itmz file (or indexing it) does not change the file association – in DEVONthink Open With it is still associated with iThoughtsX, as it is in Finder.
Sometimes when associations get cross-wired like you are experiencing it helps to select a file (e.g., an .itmz file) in Finder, open Finder’s Get Info, and change the Open With setting in Get Info – click also Change All… to make sure the change is system wide. You might have to quit and reopen DEVONthink, though that shouldn’t be needed.
Well this is curious. It had passed through my mind to do as korm suggested, though I hadn’t tried it yet. When I did, I got the result you see in the image. It asks me if I want to change all files with the extension .dt2
Any ideas? I might rebuild the Finder to reset file allocations.
EDIT I think I have worked it out – a Finder search is bringing up the files that are in the caches, but not the files in the database (which is not what I expected). All very confusing. Sorry for the false alarm.
The .dt2 files are located in DEVONthink’s Spotlight cache and are used by Spotlight to show the content of documents stored in DEVONthink database. If you double-click a .dt2 file the original file (e.g., the original .itmz file) will open in the database where it is located.
DO NOT CHANGE ownership on .dt2 files. Treat them like system files – hands off 
Marvellous – thanks for that. Just tried it and it works. A touch confusing though!