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.
Yes this is normal. You have to group shapes to make them a single object.
On an unrelated note, TinketCAD is ok to make simple shapes quickly, but once you start working with complex geometry, it quickly becomes a nightmare. Parametric CAD (Onshape or FreeCAD) is infinitely superior in this regard.
You have to group the holes with the shape you want to substract them from.
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).