The iPad is probably reporting the number of unread emails in your server's inbox, but is limited (by you, in preferences) to showing the last 50 or so emails, all of which you've read. So you probably need to use a web browser to visit your provider's webmail site and manage the unreads from there.
I had this problem on my own iPad and on my boss's. If you google this you will find so have others. I tried emptying both emails at the server and that did not work. Both iPad's still showed thousands of emails. What finally worked was deleting the account off the iPad. Doing a shutdown and restart on the iPad then setting up the email account again. The thousands of emails showed again but this time they were in the inbox and I could mark all and delete them.
I think this is a glitch in the mail program but I can't find any confirmation on that.
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