Yes, I guessed that it was related but generating the toolpath for a full surface then chopping up that toolpath simply isn't done, you chop up the surface then generate toolpaths for the parts or you cut the full surface then chop out the parts.
If your CAD/CAM isn't capable of the above you might need to cut two or more copies of your full surface to be able to machine out your parts

I don't think you realise just how complex a mathematical problem what you're asking for constitutes, it would need to

1 Recognise which paths needed to be truncated and where
and
2 Calculate which truncated paths then need linking
and
3 Would need access to the surface data in order to know how to link them without gouging your part
and
4 Generate the paths to link paths
and
5 Insert the links into the modified truncated code

The reason no one writes software to edit complex 3D toolpaths generated in another package within a boundary like this is because if they can do that they can write a CAM package that does the job properly in the first case and sell that to a mass market.

Simply buy a CAM package that can do what you need, or provide enough information about what you're trying to achieve so the guys can analyse the full problem, not just the problem as you see it after reaching your own dead end.