I know this probably won't go anywhere so just posting for visibility:
A message from a legit customer was marked as spam by Etsy and due to that I was never notified of the message and I did not see it until over a week later, I replied and marked the message as not spam.
On my account, it now lists this message as being the reason I don't (currently) qualify for the star seller badge...
This really needs to be fixed as system marked spam messages should not affect your score in any way at all..
Whilst I have not had this hapen to me (yet?) I have read others report that moving the "spam" message back into your In-box to reply will, most probably, see is as replied to after 24 hours.
A "work-around" which others have reportes as effective is to reply from the "Spam" folder. You coud also try moving the message back to "Spam", but this may block the Buyer from contacting you again.
At this time I am checking the "Spam" folder at least once every 24 hours "just in case"