I think I understand what the problem is.
Our electricity is turned off very often. the uninterruptible power supply discharges quite quickly (live in Ukraine)
My cowokers and I have about a minute or two to complete our work. BUT we manage to press the button to save the project and exit it correctly! I don't have time to shut down Windows because three to four seconds later the power goes out. In such a situation, we are guaranteed to get our problem! Tested on three different computers with ArcGis Pro version 3.2.2 and 3.3.1. We get a corrupt aprx file of normal size (or zero size with one file if it open as 'zip').
It turns out that when we click the "Save Project" or "Save Changes" button, our project is NOT WRITTEN TO THE DISK IMMEDIATELY! Probably, this requires additional time or so that some other services or programs in Windows DO NOT INTERFERE WITH DOING THIS LATER.
It's interesting that the Project Backup, which is created every 5 minutes, is deleted immediately... 😢
Developers should consider closing the project window only after the entire project has been saved to disk. If this is not possible, at least do not delete the backup.