Yes you can. They will give you credit for any days left (based on a percentage of what you originally paid and how many days are left...say you have 3 days left on a 5 days hopper, you would not get a credit for 3 individual day prices, but you get 3/5ths of what you paid originally).
We traded in our 5 day PH for annual passes after our first trip down. It was fairly painless, except that the exp date on our AP's was wrong (it was good only for 3 months for some reason - not 12 months past our "activation date") so be sure to double check your passes before you leave the ticket window. A quick trip to Guest Services corrected the problem.