I haven't done that yet with a PE set because I haven't had to, but I did do it fairly recently with a Quinta Studio 3D-printed cockpit decal set that was meant for a Trumpeter 1/32 Su-25. It was the Trumpeter Su-25 I was building, but I was using an aftermarket Aires resin cockpit set. Had to make a lot of adjustments here and there...building up side walls. adding scratch-built details to change it from an Su-25K to an Su-25M1. It was a big job, but like Greg says, it was still a lot easier than scratch-building everything. The 3-D printed decals though were MUCH easier to modify than PE, since you can easily cut and trim them with a knife or scissors.
It was a lot of work, but it doesn't look like every other Su-25 model cockpit out there, so it was worth the effort. Now if I can just get my motivation back to fix the alignment issues on the bottom of the fuselage...