I decided to delete the box but it also deletes all of the unrelated curves drawn at Step 1, which I need to keep. (Only the box is highlighted when I try to delete it, nothing is grouped.)
Also when I toggle back and forth to delete just the box using Cmd Z it deletes all of the curves with the box. It has forgotten all of the individual steps taken to create the curves.
i just guess that you used the curves and extruded it from there. you might have the option Delete Input checked, which would delete the curves right after you extruded it.
In fact I hadn’t got that checked as I like to keep all curves used for extrusions and save them to a specific layer, so that I can hide them, but use them again if necessary.
most likely a bug, specifically when the undo gets messed up. there were/are quite some issues with the undo generally but that things get deleted and are not retrievable is rather new.
i dont think that this could be a sign of a corrupted file, at least not from a hardware perspective i believe