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Is the iCloud email address linked to or accessed on any other devices?
If you aren't sure, you can check at by logging on to iCloud.com, then go to Settings and look at the My Devices section.
Ok, next you will need to try removing the email account from the iPad and add it again.
If the problem persists, check if the missing emails are going to a spam or junk folder.
Also check if any forwarding rules have been set up to automatically put the incoming emails in a particular folder, or delete them, etc.