I had this problem on my iPad a while ago. I use MobileMe to sync between an iMac, iPhone and iPad. I went into the settings screen on my iPad and opened my mail account. Rather than delete it, I switched it to OFF. I then checked my e-mail and everything was blank. Then I went back to settings and turned e-mail back ON. All my mail messages, folders etc reappeared and now work just fine
Don't know if this helps you, but it worked for me
Bill