Andy I hope this makes sense. It's actually completely new to me as my original way of doing it kept failing. Firstly I created an .stl of one of my wagons with an integral roof, it just happens to be my K1 cattle but that doesn't matter. I then open a new design and a new sketch then used Insert > Insert Mesh, selected my .stl file clicked ok and added it to my new sketch. All of which were of the end on view but I don't think that matters. Next I used Mesh > Modify > Separate to "deconstruct" the mesh giving me this: Meshbody's 2 - 8 are the separated component bodies, one of which is the roof. In this case it was meshbody8. I then hid meshbody8 and created a new .stl of the remaining parts which produced this: It took a bit to figure it all out but there's a K1 cattle with its head (well roof) chopped off as a new .stl. Give it a try, if you need help shout. As an after thought this worked because I modelled the roof as a separate body and created the .stl Mossy
As an after thought this worked because I don't combine the final bodies, so the K1 was made up of 2 sides, 2 ends, floor, chassis and roof. I hope the body your splitting is constructed the same way! Mossy
The option you need to use is MESH > MODIFY > SEPARATE - deconstruct is my way of explaining what it does.
I think as this has been made in a different program and combined it’s not taking that option. It just creates a copy