Sorry, I assumed the holes were drilled for flush ferrels. If not, then yep - you have a modification delima. One choice is filling & redrilling the holes. Not desireable, but possible. There are tolerance issues here as well as set-up time/costs. 2nd is using a CNC machine to drill the recess holes for the ferrels. There are also tolerance issues here as well as set-up time/costs. Not desireable, but possible. 3rd is using a press to push the ferrels into the existing holes & compressing the surface of the body. The ferrel lip isn't that thick, maybe 10 or 20 mils. If the body is painted it will crack around the holes. The ferrels may also deform a little. Neither is desireable. The recess won't be perfect, but sufficient. If you use a press you'll want a pin that fits the center of the ferrel to keep it's shape. You'll also want a 2nd set of ferrels. The 1st to compress the body which will be sacraficed during the pressing operation. The 2nd set will be what are installed as the finished ferrels. Last is....... A new body with the holes drilled properly for recessed ferrels!!!!! Maybe desireable, maybe not.
Good Luck.