On Mon, 14 Jan 2013, joakim@verona.se writes:

Due to a misstake I got many duplicate emails in my inbox folder.

Ironic mispeling.

They are stored in maildir format, so my initial thought was do simply md5sum the mail files and remove the duplicates. This doesnt work because the mails has differinf uids. Any other hints?

If the UIDs are just headers, why don't you simply checksum without them:

sed -e '/^Whatever-header:/d' < $file | md5sum
grep -Ev '^Whatever-header:' < $file | md5sum

Joseph Tam jtam.home@gmail.com