How do I get rid of 4,566 emails on my Iphone because of New 4.0 update?

maybe settings > mail,contacts,calendars > and either

under the mail tab adjust the SHOW option to a lower amount
or
select the email account, and adjuct the MAIL DAYS TO SYNC option

hope either of these help!

Consider yourself lucky. I have 13,500 messages that the OS 4 phone now think are new. This is a POP-mail server...typically the mail server remembers each individual mail client...so when I start using a new client, it will try to send all messages unread by that particular client. It now thinks the iPhone OS 4 is a new client altogether.

Changing the messages shown option doesn't really do anything. It will simply only retrieve the most recent 25/50/75/100/200. But as those are deleted, it starts going back in time and pulling all the older messages.

I don't have a MAIL DAYS TO SYNC option, perhaps that works for Exchange server, but not for POP.

I don't believe there is any resolution at this point. Once the POP server thinks its a new mail client...game over.

There is a small silver lining here...

Since OS 4 now has mail threading, you can delete an entire thread at a time, instead of simply individual mails.

Of course, since you can only download/view/manipulate 200 max emails at a time, this is of somewhat limited value, since you'll only be able to delete threads that exist within that 200-email view. YMMV on how much savings you get, but hopefully your delete-clicks will be somewhat less than the actual number of emails being reported because of this.