[MJK]

If I understood correctly, then I had that problem in 1.0 and I haven't tried and will not try to do it again.

What I did then was I added an item to the Inbox with a link, the link went to the comment as it always does (the Clippings does it too). Then I tried to drag that link from the comment to the sidebar in Planning Mode, where all my projects are. I was trying the functionality of OmniFocus, partially actually in order to find bugs and it did indeed turn all my items to links and I couldn't undo it any other way than to remove my settings files.

If someone wants to try to reproduce it, that would be the way to do it.