Bramleycox..
There are two types of mail accounts: IMAP and POP3
From my understanding of POP3 accounts they do not communicate the tag that a mail item is read.
In other words.. your mail is on the yahoo server, if you go and look at it at yahoo and read through the mail it never will tell your phone, ipad, or anything else that this mail is "READ".
On the other hand when you open your mail account on an iphone or android or anything else for a POP3 type of account the DEVICE will remember what you have read and haven't because it was read on the device itself. (these mails in the case of pop3 accounts are actually COPIES of your mail and not the actual mail).
So... then later on down the road you install a major update. Since neither the yahoo servers nor the iphone communicates to the server that POP3 mail has been "read", when you re-add the account you will have all "unread" mail again.
I tried to explain that in simple terms.. but the simple point is - It's the nature of a pop3 account. (I'm not speaking of the "phantom mail" error, I'm speaking specifically of the situation where you re-add your account in a major upgrade and the mail is remarked as "unread").
It's how POP3 email functions. So, this would be why Apple hasn't addressed it.. because that particular behavior is expected and not related to the device.