If you own our EMAIL SUPPORT add-on, you can configure the subject line of your emails to include the specially formatted ticket number. Then, users can respond to the auto-close message and have that logged directly to the ticket. Simply add this to the subject line (#{ticket_id}#)
All flags for sequencing of emails and status of emails sent are held in a metakey on the ticket with the name ac_sent_wmsgs.
The last time a ticket was checked or processed is held in a metakey on the ticket with the name last_autoclose_process_date.