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 believe that *in theory* it should work like that, yes.

A few times I've had a rep recalc and still had what appeared to be some oddities. Here's a sample timeline:

* 2am: 5 genuine votes
* 3am: 20 upvotes from one user, hit cap after the first 15 of them
* 6am: Get online, post answers, get more upvotes, report vote fraud
* 10.30am: Votes are removed, 150 points lost
* 11am: Request rep recalc: still not hit rep limit despite having lots of votes

In other words, votes that didn't count due to the rep limit being hit for fraud *appeared* not to count after the rep recalc. I had a summary screen for "today" which showed *less* than 200 rep, but still votes that didn't contribute to reputation.

I'm not overly bothered and it's a very hard thing to diagnose for certain, but that's at least what I *think* I saw. It does sound very odd, based on what a rep recalc is meant to do...

Now, the good news is that all of the votes are recorded so if there *is* a bug in the recalc procedure, when it's fixed and you get another recalc, you'll get the rep back.

I believe the *intended* behaviour is for those "wasted" votes to come back into effect after previously-counted votes are deleted, at least.
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.