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.htm
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
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