Problem with large inbox email.

There's little you can do about this, unless you want a lot of work. POP3 is not meant for storing email on server and this is why. You can either:

1. Empty out the inbox and they lose the email

2. Check through their email and see if there's a few huge emails that can be deleted using mutt:

mutt -f /home/acount/mail/domain/username/inbox

3. Take a copy of their inbox file, empty out the live one and slowly copy and append chunks of emails from the copy into the live one using your favourite text editor

4. Have the client use a utility like Mail Magic Monitor where they cann connect to their POP3 account and delete unwanted email so that their mailbox is reduced to a managable size where they can download what is left:
http://mmm3.sourceforge.net/