Thanks for the clarification!
I've looked at quite a few different Twitter follower tools and ran this by a couple of other people on the community team and I've pretty much come to conclusions #2 or #3 that you mentioned. Unfortunately, there's just not really a clear cut way to figure out what happened. Sorry I don't have a more definitive answer.
You might want to consider tracking your account in Followerwonk going forward if you aren't already. It's a good way to see if you've lost a bunch of followers, who those followers were, and look at the date to see if you posted something in particular that could have led to a dramatic follower loss. Doesn't really help your current situation, but might help if anything strange happens in the future.