Question: Today, I reached 200 rep, but 20 of them came from a now-deleted post (a duplicate answer posted really close in time to the first answer). I stopped getting rep from my answers after this was deleted and I hit 180 reputation on posted answers today (180 + the 20 from the deleted = the cap of 200).

After a rep recalculation, I will lose the 20 points from that deleted answer (I'm pretty sure). But will the system detect that I made more than 20 points after that and give me any rep from after that?

The only reason I care is because I want to reach 20k before the Boston Dev Days...

Personal Example:

* 200 rep earned to hit cap
* 3 more upvotes for 30 "potential rep"
* Answer deleted wipes out 2 upvotes to drop down to 180 rep.
* Rep limit after recalc **should** come out to 200 with 1 upvote left over due to cap.

Answer: 
If you keep getting rep for today then it will count toward the limit for the day after the recalc. So if you got a total of 220 today but 20 went away in a recalc then you would still get 200 for the day. The system still tracks your rep for the day even after you hit the limit. It just doesn't apply more than 200 per day.
I think so, a rep recalc computes all your reputation from scratch, so the rep cap would be taken into account without counting the now deleted post and you'd get the reputation from the subsequent posts