I've had that before - so have some of my colleagues. If you don't save, it seems to get worse, and each future save has more and more unknown elements deleted. Then it gets to the point where you can't save at all because the error message keeps popping up till you say don't save.
Here was my trouble with it.
Anyway - my advice is to go to your last bpn (hopefully you haven't saved yet) and copy it somewhere else and give it a new name. This was your last uncorrupted version of the file.
Then, save your current file if you've done a lot since the bpn.
Open a new and reset project from your template and do a forward merge. You'll lose all your 2D info pasted into section/elev/detail windows (as mentioned in the thread I linked) but you can get most of this back from your bpn (now saved under a different name). Depending on the size of the project, you may lose a couple of days to sort all this out - but I still think it's better than losing the entire project due to some unknown corruption.
Good luck!
