[Cialug] System "reset"??

[L. V. Lammert]

OK, .. here's a really good one! I rebooted the Pi that runs the PBX we're
playing with, and I noticed that a package AND it's config file is
MISSING!!

Looking at syslog:

Jan 24 16:17:15 PBX systemd[1]: Reached target Login Prompts.
Feb 15 18:11:02 PBX ntpdate[452]: step time server 173.71.80.235 offset 1907624.755086 sec

How can EVERYTHING on the system be reset to 1/24 without farlking the
file system??????