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: 
I think you should get that rep back. I want to believe that if you got 25 upvotes in a day, you should cap at 200. If you had an answer deleted that subtracted 2 upvotes that left you with 180, you should still in theory have 230 rep worth of upvotes, so during a recalc you should still make the 200 points.
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