From what you describe, you likely have an issue with how your email is configured to your iPad (e.g., not configured to delete from the iPad when an item is deleted from the server). But you do not have a BlackBerry problem. So your inquiry would be best directed to forums/sites that specialize in iPad issues, not BlackBerry issues.
Occam's Razor nearly always applies when troubleshooting technology issues!
If anyone has been helpful to you, please show your appreciation by clicking the button inside of their post. Please click here and read, along with the threads to which it links, for helpful information to guide you as you proceed. I always recommend that you treat your BlackBerry like any other computing device, including using a regular backup schedule...click here for an article with instructions.