Does you email provider support IMAP? If so, IMAP is a considerably more flexible (and modern) email protocol. IMAP is also better suited to situations where you access email from multiple devices (e.g., iPad, iPhone and PC/Mac).
POP3 can be configured, in broad terms, in one of two modes - these being Download and delete from the Server, or Download and leave a copy on the server. These two modes should be largely self-explanatory - the former making mail synchronisation across multiple devices almost impossible. When using POP3 with multiple devices, you really do need to understand the nuances of your settings.
Where your email provider supports both POP3 and IMAP, it is possible to run a mixed configuration - with some devices (usually mobile devices) using IMAP - whilst perhaps using POP3 with a PC/Mac to maintain a local email archive that is independent of the Mail Server.
Using IMAP, the original email “lives” on the Server - each device downloading/synchronising a local “copy” to view. When an is deleted from any IMAP-configured device, both the local copy and original are deleted; other devices automatically synchronise.
Returning to your actual question, the easiest way to prevent unexpected return of deleted email is to convert to using IMAP. Otherwise, more detail of your actual iPad settings will be needed if we are to better understand your issue.