Your problem descriptions and what you are doing is very unclear to me. I don't know what it means if "all parts fall apart", and I have no idea what you tried to get them back together or in which way you modified them. It is unclear as well which steps you performed to export to pdf.
Of course it is helpful to have the big picture where you want to go, but if we should assist you we need more details what exactly you did. A helpful description tells almost every click from the start of FreeCAD, such as
- switch to workbench xyz
- select obj_abc in the tree
- select face_ejk
- apply function fuse, slice, cut, ...
This is done up to the point where your expectation and the result differ.