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Hm... sad to hear something like this is happening. This is, of course, neither intended nor expected behaviour, and though it won't help you much, I can guarantee that this is not happening here nor on any other machine we've tested.
Before trying to find the culprit, you could try and ctr-click (or right-click) on the project in question and select "show package contents" from the menu. With some luck, you might find all your drafts and articles inside in some folders.
You can also check ~/Library/Application Support/Ulysses/Backups and see if the intact version of your project has been placed there. But work on a copy, please...
Dirk or Max will get back to this thread today and see if they can be of further assistance.