There is an option to remove Deleted Messages after a certain time. But I doubt that is what you are talking about. In case it is, you'll find it under Settings > Mail, Contacts, Calendars > Your Account > Advanced.
Out of curiosity, when you scroll to the bottom of your Inbox list do you see a Load More Messages options, and do your older messages get loaded when you tap it?
You can try turning off you Mail sync in your Account settings. Open Mail to make sure that your account went away, then go back and turn Mail back on in the account.
These other common fixes might make a difference as well:
--------------------------------
When you have problems with an app it's a good idea to clear it from RAM.
Close/Clear the app: With the problem app closed, double tap on the Home button to get the multitask bar. Tap and hold on any icon in the bar until they jiggle, then tap the minus sign on the problem app. This will remove it from RAM and insure a clean start the next time you launch the app.
If that does not work try a restart,
Restart: Hold down the power button until the power off slider appears. Slide it off. When the iPad finishes shutting down, hold down the power button again until the Apple logo appears. Apple recommends you restart the iPad at least once a month.
and then a reset if that does not work.
Reset: Hold down the power and home buttons until the Apple logo appears. The iPad will reboot. This usually takes a bit longer than a restart.
