I had a similar situation last year where I cut several long-haul segments off the end of a very complicated One-World award. Working with a very cooperative AAgent in the Dublin office, he recalculated the flown segments and exchanged my partially used ticket into a "cheaper" award. The difference in mileage was returned to my account, and I even got a refund on the taxes.

I did not pay any service charge, though this whole situation arose due to uncooperative scheduling changes with BA which led to the decision to cancel the final segments, so there was an element of goodwill in the AAgents activities.