I have just had this happen to me. Twice!
Also, when I tried to run emplode again II got a message saying that the database was locked. I had to reboot to get it to run again.
Isn't it possible to have some sort of journalling system, where changes are recorded, as it is incredibly annoying when this sort of thing happens! (Yes, I know it's a beta :-) but similar things happened to me on 1.x releases too)

Phil.