I made this test block to test the fit on some holes (my printer isn’t calibrated), when I noticed the problem. The cone on the side was a sanity check for this problem.
I tried googling but couldn’t come up with this same problem.
Edit: I did just figure out a way, I made them a union group, which applied the cuts immediately, and they stayed when exported. I’ve never had to do that before. Though admittedly that’s probably the right way, I normally use fusion360. Something is definitely weird though. It should just work without doing that. And in fact it did a few days ago on a different project file.
Fusion 360 has been great for me. The modeler is very easy and practical for simple folk like me. I use their free edition. I had the paid subscription for a year but then went down to free, which works just as great.
Unfortunately Fusion360 has no official Linux support and is not easy to download and install, while Onshape is browser-based so OS-agnostic.
The paid version does allow for use from a browser, which I used from Ubuntu a lot. That’s how I got into Fusion360 after headaches with Onshape, FreeCAD and many others. The Fusion360 modeler is very good, and parametric.
However, I understand this solution might not work for you.