[Dovecot] Move mail in Maildir without IMAP

[RW]

I set-up some spam/ham learning folders where a crontab entry learns
the mail and them moves it do a different Maildir folder.
Unfortunately, since it has a different dovecot-keywords file, any imap
flags get changed to unknown-0, unknown-1 etc. 

I tried the following, but it didn't work 

mv "${src_ham}"/cur/* "$dest_ham"/new/
cp "${src_ham}"/dovecot-keywords "${dest_ham}"

Is there a simple way to do this correctly without going through IMAP?

And are there any more serious consequences of moving mail like this,
with dovecot imap running on top.