Hey Sabatino,
Thank you for reaching out to the community. The Flags etc are stored in the mailbox.cfg. It is also not recommended to move or touch any files while the service is running. I recommend that you use MailStore or another backup solution.
Please let me know if this helps.
Kind Regards,
Zach Sylvester
System/Network Administrator
SmarterTools Inc.
(877) 357-6278
www.smartertools.com