Moving it out back to public GH was done by transferring the repo(s) between organizations. The move into GHE moved the organization as a whole to GHE. So it's conceivable that moving organizations as a whole to (or even from) GHE does not send emails. To be clear that's still bad, especially given how the user could only know of this move if they were logged in and looking for one tiny bit of text in the repo homepage, but it's a non-malicious explanation.