Yeah, my son called to have the park hopper plus portion of his 7 day ticket refunded and only got $30-something back. Neither of us could recall what it actually cost to add them on as he bought the tickets over a year ago, but we're pretty sure it was more than that. It appeared to us that Disney simply refunded the difference in what he paid vs what a ticket costs today (after 2 price increases since he purchased the ticket). I could understand that logic if park hopping and water parks were still available and someone simply changed their mind and wanted them removed. But as you paid for something that Disney cannot provide, they should have refunded the actual cost of those things when the ticket was purchased. Oh well.
At the end of the day - like you said - it's not worth spending vacation time fighting with them over it. I imagine their system isn't set up to do handle it the way we'd like so my son just took the refund they gave him and moved on.
Enjoy the rest of your trip!