Welcome to Android Central! Do you mean deleted from the phone, or from the mailserver?
In general, it's better to use the IMAP server for an email provider, rather than POP3. IMAP is newer, and syncs with the server, while POP3 is older, and physically downloads the email from the server to the phone (and then often deletes the email from the server). See the difference here: IMAP vs POP3. Here are the IMAP settings for Hotmail: Set up an email app with Outlook.com - Outlook.com Help