“It’s like deja vu all over again.”
Something that can happen very easily regarding the references you store in your idea collection are duplicate entries: the same image, document, etc. is inserted twice (or multiple times). And easy way to prevent this in DEVONthink is by using a smart group looking for duplicates in the Inbox only (Note the “Search in: References Inbox”).
I use a database named references and limit the scope of the smart group to its inbox. Whenever I put something in the inbox (new images, files, etc.) DEVONthink compares it to the content of the database and if it finds a file with the same content, it makes the filename bold and blue — and it appears in the smart group.
This way I can simply select and delete the duplicate entries in the smart group and remove the newly copied files, without touching the files that are sorted in my collection.