I have resolved my issue
Storage location of mail data:
Username > Library (Hidden folder) > Mail > V2 > Mailboxes > Notes.mbox > ID String
There were two ID strings in there so somehow my mail did something odd as I don't recall changing mail or cloud or anything else related but that doesn't mean I didn't...
A simple copy/paste from one ID string to the other, open mail, select account, then Mailbox > Rebuild and all my notes are back where they are supposed to be.
Hope that helps someone else in the future.