Looking at the log you can see how your server is deleting the bounces properly. eMail Bounce Handler sends DELETE commands and your POP server responds with successful deletion messages. 'DELE' commands are issued by eMail Bounce Handler followed with the message to delete number. Each time the POP server responds with "+OK message deleted" that means a successful deletion. This string is not generated by eMail Bounce Handler but by your POP server. eMail Bounce Handler just display this result through the connection log.
This is the complete sequence:
10/1 17:29:39 > RETR 28
10/1 17:29:40 Mail Subject: Returned mail: see transcript for details
10/1 17:29:40 [•] Bounce detected
10/1 17:29:40 > DELE 28
10/1 17:29:41 +OK message deleted
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