First of all you need to know that POP3 protocol doesn't have a concept of seen/unseen emails nor folders.
If you need to delete an email just use Pop3.DeleteMessageByNumber or Pop3.DeleteMessageByUID method.
Gmail's POP3 server is not a regular POP3 server however. It can work in several modes depending on the account settings. Those change the way accessing and deleting messages work greatly:
https://www.limilabs.com/blog/gmail-pop3-behavior
We strongly recommend using IMAP for Gmail access.