They sell the stepped drill, but I’ve honestly never used it. If I run into issues with a Confirmat screw, I usually just skip that hole, drill a new pilot hole with a standard bit, and use a regular 3″–3.5″ construction screw as a replacement. This works well, especially since Confirmat drill bits are very long and can be difficult to work with on site.

If the holes are off on a single part, then the part likely shifted while being drilled on the CNC. The smaller the part, the easier it is for it to move/shift during drilling.

If it’s just one part that’s off, I’d simply drill new holes and use Grip-Rite screws from Home Depot. The 3.5″ version works great—they have a coarse, aggressive thread that bites very well.

https://www.homedepot.com/p/Grip-Rite-10-x-3-1-2-in-Star-Drive-Dual-Flat-Head-Coarse-Thread-Construction-Screws-5-lb-Box-312GCS5/204959272

The same 3.5″ screw works well for installing cabinets to wall studs. About 1″ is taken up by the cabinet back and the 3/4″ nailer, leaving roughly 2″ of the screw solidly embedded into the studs after accounting for the 1/2″ drywall.