I booked a three day weekend at a good rate.
The rates have gone up and now a two day weekend rental is much more than the rate I got for three days.
If I end up returning early after two days, does that trigger a recalculation and charge at the current rental rate, do they keep the old daily rate and charge for two days, or do they charge me for the three days of the original rental?

Most likely no. You generally get locked in at the rate you booked and if you return a day early, it's not going to affect the original base rate. The rate won't get recalculated unless you are on the border of a weekend rate and a weekly rate or something like that.

I think in this situation you won't pay any more than what you originally reserved now. Now the other question is whether you will pay 2/3 of the rental cost if returning one day early on a 3-day rental. Often the answer to this is yes, but it can't be guaranteed as sometimes the rental company may charge you for the original contracted amount, especially if you're renting for more than 48 hours total.

Where it could matter is if you applied some coupon that requires 3-day minimum or something like that. By returning early (or late depending on the coupon terms), you may invalidate it.

In short, you should be fine.

I am not sure there is a way to know. I had a "free weekend" certificate once and returned the vehicle less than 24 hours (1 PM Saturday to 11 AM on Sunday) and got charged because that wasn't a "weekend".