I don't know if this helps, but I thought I would document it here. I was having similar issues about trying to get all my Apple devices in-sync. Especially if I deleted mail and had to keep deleting all across the board. I am on IMAP so it should have synced. But I couldn't figure out why it wasn't.
Finally discovered the solution. In you iPhone and iPad device, you need to update the default settings for mail. Go to Mail, Contacts, Calendar ->select the email account -> Select Advance (at the bottom of form) -> Mailbox Behavior! Under behavior, you will notice that the default setting is to save on my iPad/iPhone. You need to change this to ON THE SERVER for each folder (DRAFTS, SENT, DELETED and ARCHEIVE.) This will keep your mail synced.
I think Apple uses that as their default as they aren't sure if people are backing up their email. I know when I delete my messages, I want it gone.
Hope this helps future generations as well as you.