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Setup imap and drag and drop into the new account in a mail client of your choice?
Or use Google takeout to download all your apps data in one shot.
http://www.lowendtalk.com/discussion/64631/how-to-backup-an-external-imap-account#latest
This might help you
@jar would maybe able to help you with his experiences.
imapsync would do great for this
http://www.linuxbrigade.com/migrate-mail-one-server-another-imapsync/
I've used gmvault with great succcess (and supports resume/periodic syncs, etc):
http://gmvault.org
Thanks for everyone who recommended imapsync. Just used it to migrate all my mail from a google apps account to a self hosted account. Love it!