There seems to be a strange bug in 4.4.2 where mail is not syncing and is marked as unread with the email server, in my case an IMAP server where every other place is synced correctly (Mac Mail, Google Mail, webmail, other devices).

I managed to fix it by changing the mails “sync period” to one day (one day of emails displayed on the phone). To try this yourself do the following:

• Open the mail app
• Open the menu and select settings
• Select “Account Settings” -> Select the account -> Select “Sync Settings” -> Select “Period to sync Email”
• Change the period to 1 day
• Back out of the settings screens, back to the email view.
• Sync your email, it will hopefully all be working again now.