What happens when a customer uses two different account? I responded to his messages on the main account he used and he sent messages from his other account as well and since I responded to the account that he ordered from, my message percentage was hit. How can that be fixed?
Unfortunately, it can't really be fixed without sending the message to spam. What I do for messages like that is just a quick "Hi ___, I've responded in your other message" That way you're acknowledging the message, but don't have to sound redundant.
@James6Creations: The Star Seller metric for messages is very simplistic and binary - either you replied to (or marked as SPAM) that first message of every new incoming thread within 24 hours or you did not.
If the unanswered new thread is not a Help Request, at least for the time being, it appears that marking an unanswered new thread as SPAM (even after the 24 hour deadline has passed) will cause your reply percentage to change in a day or two if the original message was within the current star seller period (but not retroactively). Note that subsequent messages from that account may go directly to the SPAM folder.
You have to reply to each new message thread,
so just reply