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If the embedded links are not taking you to the right files in Dropbox, then it sounds like the problem is with Dropbox, not with OF. As an alternative, you could try Evernote. Evernote can store both traditional text-based notes as well as files embedded within the note. While in Evernote, you can copy a link to the note and then paste that link in to OF. I've never had an issue with Evernote links not working properly, so I suggest giving it a try.

I understand the wish to store all of your support materials within OF (essentially what David Allen describes as "Reference material and Support information for projects") but realize that OF is a task manager, and not a filing system, document management system or any other sort of long term file storage solution. There are MUCH better systems out there that focus exclusively on document management--you can look into solutions like Evernote (mentioned above), Zengobi's Curio, or DevonThink.