Would it be that the calendar overwrites the whole file?
No, that’s not possible as far as I can tell. This file is handled by timed alone. There is no concurrent access. The calendar is asking to add or remove alarms via timed client library (which talk to the timed daemon via D-Bus).
Nonetheless, that’s an interesting observation. It’s not a file systyem issue, or the file that is not present at reboot, or whatever related to this file. The fact that the calendar alarms are still there (and the calendar never “reset” its alarms on reboot), means that something is removing all clock alarms, either during shutdown or during restart… That’s a lead to follow : finding what part of code can flush the clock alarms and see what can trigger it.