Yesterday I was very happy because my total rep was over 40000. This morning I was stunned seeing it had dropped to 39693.
Does anybody know what happened?
There's a script that looks for "suspicious" voting patterns between users. The details are kept intentionally vague, and normally you shouldn't ever be aware of it...
But it is possible - and in this case very probable - that 63 up-votes cast on your answers by another user were nullified early this morning.
Sadly, as one of the top users on the site, you're more likely to encounter extreme edge-cases like this. Normally even if you did notice an abrupt drop in reputation from something of this nature it would be for a much smaller amount... But in this case, my suspicion is that a regular user got a bit too enthusiastic about several of your answers and spooked the scripts big-time.