I’m thinking this through. (I’ve been in Graphic Arts / Printing for 28 years now so I am well aware of what you may be hoping to / needing to do.) The immediate problem I see is that the “folders” in DEVONthink are not folders. They are just a convenient view of files that are in a very different structure under-the-hood. This makes linking within DEVONthink very difficult. Not impossible, but difficult in the normal course of things.
This is also why your links break. If you link to a file on your desktop and import it into DEVONthink, the absolute link is still intact. When you delete that desktop file to clean things up, the link is broken. Trying to resolve the links would be a frustrating exercise.
A more likely scenario would be to work in indexed folders on your machine. But remember that DEVONthink is made for categorization and search more than file management. It is not a Finder replacement, as some hope it to be.
However, say you imported a folder containing an ID doc and an image. Command-D to place in ID and, if the DEVONthink database was visible, you could drag and drop from DEVONthink to the dialog in ID to link the file. This would be a valid link (though I’d have to test if a database Rebuild would change the file location for some reason)
- Remember too that ID will create temp files when you open the document. If you have an ID doc open when you close the database, there is the potential that it could be treated as an orphaned file. When you close the ID doc, the temp file will be deleted. Checking the database, it appears all is well but I would be work cautiously at first.