Also having this issue. Probably lost a dozen missions - for a while I was saving each mission twice (e.g. "Mission Name" and "Mission Name Back Up") and when one was erased I would load the other and save over the erased one. Eventually both came up empty at the same time. I haven't noticed anything consistent that seems to be causing it.

Sounds like the exact problem I am having. It doesn't make the editor completely useless, but if I want to test the mission more than once then Arma has to be restarted. Hopefully it gets fixed soon!