I had some luck with this yesterday.

Attempt #1 was editing in blender, and it took 3h to get the file to slice correctly (I needed to remesh in blender sculpting tools to get the overlapping shapes to work).

Attempt #2 was importing the STL in openscad and doing a union() of the two objects. That worked perfectly the first time and took 20min. (But it was way more annoying to pick exactly the right number to translate all the shapes around)