Get some foam (preferably fire-resistant), a lot of masking tape, and a heat gun. Wrap your blade and whichever parts of the handle touch the sheath in masking tape (not enough to interfere with its shape in the sheath), remove any removeable hardware from the sheath, and get something set up so you can press the foam around the sheathed knife when that's ready to done.
With all of that set up, fire up the heat gun. You want to heat the kydex to the point where it can more easily move, but not to the point that it's like melted cheese (if it's hot, but you can't smell the toxic PVC fumes, that's the way to be). Place the knife in the sheath and use your fingers to mold the sheath the way you want it to be. When done molding, place the knife between the two pieces of foam, place the two pieces of foam between two hard, flat objects that withstand a lot of pressure, and apply a lot of pressure (setting up a bunch of clamps on a few boards is always good). When it's done slowly cooling down in the foam under pressure, you should be all set. That's how I got the kydex insert in a sheath to fit a barely oversized blade (thanks, SARHound!) and it happened with minimum swearing.