I would wash the bag with Nikwax Down Wash on low in a commercial front load machine. Dry 2-3 hrs on low heat with a few tennis balls to break up any clumps and get it dry to touch throughout the bag (feel it every hour or so and see if you can feel and wet clumps of down -- if so you need to keep drying it).
Once its washed that should help it maintain its max loft -- then cut off the top portion you don't need, invert the edges of the fabric and pin in place -- adding a drawcord channel (or simply cutting off the existing drawcord channel at the hood with enough fabric below it to flap over the new cut edge - and resew together. I've gone it and its not that bad.
IF POSSIBLE try to cut right above (1 inch or so) an existing baffle to help keep the down from coming out when you cut it open. (down will still come out - but not from the lower portion of the bag, which is what you are saving)