Using version 4.80 on Windows 11. Installed again on a new computer. Is there a setting where email will be deleted on the server if I delete it using PMail?

That depends on how you are connecting to the server. If by POP3 then no, deletes on Pegasus Mail do not affect messages on the server. However, that can be controlled in the POP3 host configuration. If connecting by IMAP then yes, deletions on the server are possible. There are several options so I think it best to refer you to pages 144-145 of the Pegasus Mail manual for the details, or the IMAP category in Pegasus Mail Help. You will have to follow the links to "Defining an IMAP profile" and then "The "Settings" Page" to get to the details about deleted message handling.