If you already have some mail in your maildir and you have set procmail filters, then it is difficult to apply the procmail filter, right? Not so, you just need to go to the Inbox directory and then execute the command.
for i in *; do cat $i|procmail; rm -f "$i"; done
This will pass all of your e-mail through procmail again and then your filters will get applied. Mails will go to their appropriate directory and you will be one happy man, I hope.