Hilton does this sometimes, it's a royal pain. Sometimes one night will be a different rate then the other nights, but most times they just adjust all the rates to the highest rate.

I would first call the hotel and see if they can adjust the three night reservation to reflect the change in rates.

If not, it can be a hassle if they expect you to check out by checkout time and check in again if they don't get it right at check in or have assigned you to a different room each night (yes they may do that). They will also process it as three different transactions, three different holds on the card, etc.