I have had some airplanes with a split cowl and some with single peice cowls. I've never had an issue getting a one piece cowl over a twin. Maybe a picture would help me understand your need. I will be more then happy to describe a method but it will be a fair amount of work.

Is the cowl you intend to split fiberglass?

Mark your cut line with masking tape and then very carefully cut the cowl with an Exacto razor saw. The saw is the best way to do the cut because you will loose the least amount of kerf. Sand the edges straight wilte not removing too much material and slightly round the edges. Sand the inside edge of the lower half really well with 220 grit and clean. Take the upper half and tape the edge with thin packing tape. The tape needs to be applied 1/2 on the outside and then wrap around to the inside. It will help the tape to stick to the inside I'd you sand and clean the same as the bottom half. Apply carnuba wax to the tape. Next tape the two halves back together using packing tape on the outside only. What you have now is your cowl temporarily taped back together with the inside top protected with packing tape. Now using epoxy laminating resin and 1" fiberglass tape, lay a couple strips of the 1" fiberglass tape across the cut line and allow to dry. What you are doing is molding a lip on the inside of the lower cowl. When the epoxy is dry you can seperate the halves as the epoxy will not stick to the waxed packing tape that you applied to the upper cowl.