Most likely, what happened is that you triggered a rep recalc. On normal SE sites, this isn't a big deal because deleted posts are accounted for automatically and recalcs rarely result in more than a small amount of rep being lost. However, on Area 51, you keep the rep from questions/follows/commits on deleted proposals until a recalc occurs. After the recalc, the system treats it as if those deleted proposals never existed at all, so you lose any rep from deleted proposals, and it happens suddenly and seemingly randomly.
I lost around 500 rep to one recalc a few months ago. I'm certain that was the cause, since it was triggered by an account merger which always results in a rep recalc. Other users have lost much more than that. For example, warren was at nearly 10k rep at one point, and is now at under 5k. This MSO post is by wikis who lost 2k rep from one. Here's another example on Discuss Area 51 which says that this is status-bydesign.
As far as I know, there's not much you can do to prevent a rep recalc from being automatically triggered (though you could trigger one yourself by going to http://area51.stackexchange.com/reputation and clicking the recalc button). As of right now, the only way to be sure you can keep your rep is to make sure to keep proposals active until they hit beta so they won't be automatically deleted.