I know what I am asking is a bit weird question, but while surfing around I found the highest reputation gain in a single day. I thought: why not try the highest amount of reputation lost in a single day. Who lost the most reputation in a single day?
On September 25, 2015, a user on Mathematics.SE lost 33,934 reputation in a single day as a result of three events:
- 33062 rep lost from a removed user
- 660 rep lost from a different removed user
- 2 rep lost for a downvoted answer
I'm not sure if you count suspensions, where a user's reputation drops to 1 for the duration of the suspension period. I know of users with more than 90k reputation who were (quite recently) suspended.
If not, @rene mentions a case which affected almost the entire Stack Exchange network since the deleted user cast a lot of votes on a lot of sites. If you browse questions posted on child metas around that time, you'll see a lot of screenshots by people losing reputation.
But I'm not sure if that event led a user to lose more than 1,000 reputation on a single site; here is a case where somebody on English Language & Usage lost 2,134 reputation because of a user deletion.