Between 18 Aug, 2022 and 30 Aug, 2022, reply notifications that included a custom footer did NOT include the text "Reply above this line to add a comment."
This caused the reply to be improperly parsed, assumed to be an automatic reply, and dropped.
There's not a way to retroactively fix notifications that have already been sent, so it's expected that as these older notifications "age out", the issue will naturally resolve.