It is possible, and altering the script so like so
Code:
print "----Done processing message, stored in mail_$dirname$count.txt----\n\n";
} # end if subject not internal data
} # end of for $msg
system ("/opt/zimbra/bin/zmmailbox -z -m $user addmessage /$dirname /tmp/$user/$dirname/");
} # end of flagset=1 does work, I tested it with a couple of mailboxes without issue. However, if you were to encounter an error like I listed in my first post it stops importing for that folder altogether and moves on to the next folder.
I've re-adjusted my script back so that it's uploading on a per-message basis and logging the output so I can see which message is causing the error.