@tobiaseigen helped me debug this issue. It’s due to the bug introduced in 1bb485f and fixed in d51019e.
All emails sent between these two commits (only a couple of days) will not have the user associated to the email log. Which means that whenever we process an incoming email that uses a reply_key, it won’t match any user and will thus be rejected.
I just pushed a migration that should fix all the email_logs that were created between that period and I highly recommend that you guys upgrade to latest ASAP if you haven’t already.
https://github.com/discourse/discourse/commit/de58e58272b73fa08c193e444605c0153224115a