We just did this in September with a discounted park hopper that we bought at my husband's work (law enforcement). We paid $63 for a park hopper so we could go on a blackout day and then they applied that amount towards our So. Cal. Select annual passes. We just paid the difference at the park.
They will apply the amount you paid. So, if you got a discount on the hopper,you'll get that amount credited to your a/p, not the undiscounted value of the hopper. Hope that makes sense!