I always use union-groups when working with holes. Sometimes I even have to go through multiple nested union groups to get the desired result. But it always works when exporting, and you directly see the resulting shape in the editor (and the export).

I don’t run Linux , but I love Prusaslicer and it is available for Linux: https://flathub.org/apps/com.prusa3d.PrusaSlicer

Кашкавал (kashkaval)

It’s funny how everyone answers the question, yet you still don’t know which language it is