I didn't try with SM 13, but with previous versions, moving large number of emails using the web interface usually leads to problem (duplicate messages etc...).
I was using the following steps :
- Stop SmarterMail
- From windows desktop on the SM Server, move the files from the old folder to the new one (folder must be existing, if not, create it from the webmail before stopping SM, do not create it from Windows)
- delete the file mailbox.cfg in both folder (old and new one)
- restart SmarterMail
It seems SM 13 better handle this now, you can check the KB here :
look at the "Restore a User's Emails / Move a Large Number of Messages" part of the document.