First, assuming that you are using an IMAP mailbox, verify that the missing email is still saved on the email server. To do so, sign-in to your Mail providers webpage - and check that email is present.
If you have established that the email missing from your iPad is still available on the mail server, the simplest method of restoring all mail on your iPad is to delete the email account from your iPad, restart the iPad, then re-add the email account.
To remove the email account:
Settings > Mail > Accounts > [Your email account] > Delete Account
Restart your iPad:
- On an iPad with a Home button: Press and hold the top button and the Home button at the same time. When the Apple logo appears, release both buttons.
- On other iPad models: Press and quickly release the volume up button, press and quickly release the volume down button, then press and hold the top button. When the Apple logo appears, release the button.
After restarting your iPad, re-add the Mail account using the Add account wizard:
Settings > Mail > Add Account