I just setup Mercury on Xampp and I am trying to retrieve emails so I will have the emails on the Mercury server to read with Roundcube. I was able to download the emails but the original emails are deleted. I put a check on the MercuryP pop3 server setting to "ignore Pop3 delete commands", but the original emails were deleted on the client server. Apparently I have something set wrong. I do not want to delete the original emails.

Also, I cannot send emails to the original client now?

If you are collecting messages from another server using the POP3 protocol it's handled by the POP3 client module (MercuryD). Check if it would be possible to instruct the server on the other end to keep messages after they have been downloaded.