There are many different ways to dealing with this. Here are the ways you can deal with this:
1. Grind it out to fit. Downside is this may allow for slight tooth movement.
2.Grind it out then take an alginate mold pour it up in stone. Place the appliance on the stone and make sure it fits on and off easy. Next super sep the cast and then mix acrylic and monomer into putty and place in the appliance and sit it back onto the stone model. Soak in hot water for 20 minutes then remove from stone and trim and polish.
3.You can grind it out and then using a chair side denture reline acrylic add to it in the patients mouth. Tokyama rebase.
4. Send to the lab with an impression for a correction.
5. If it is accufit from Dynaflex then just boil it to heat the thermoplastic and re-fit it in the mouth.
6. Make a new appliance. If over 5 years old I do this.