In order to conserve space, the emails that you move to folders are not stored on the iPad indefinitely. When you open the folder it can take a little bit for the iPad to contact the email server and download the folder's contents again. Pulling down on the email list can hurry this process. A little waiting animation shows up at the top while the email is downloaded. (it's called pull to refresh).
If there are a lot of emails in the list you'll see a Download More (or something like that) when you get to the end of the list.
If you try to access these email folders when you do not have an internet connection, it very possible you won't see anything in the folder at all.
If none of this applies, pleas add some more details, like who your email provider is and how you are moving files to folders (in case it's something other than what I'm thinking). You iOS version and iPad model might be helpful as well.