Git mysteriously runs Garbage collection "from time to time" and deletes and orphaned commits you have.
https://www.kernel.org/pub/software/scm/git/docs/git-gc.html
Scientifically, this will occur approximately 6-8 hours before you realize you really needed that commit which was just deleted.
I'd rather not have my files deleted by Git. How can I disable automatic garbage collection altogether?
From the very same page you just linked to:
Some git commands may automatically run git gc; see the --auto flag below for details. If you know what you’re doing and all you want is to disable this behavior permanently without further considerations, just do:
$ git config --global gc.auto 0