Apple mail and a POP3-only mail account I have set up a mail account with Apple Mail. What I realized only when it was "too late", the mail server does not provide IMAP (only for a fee), and thus roundabout 100 E-Mails were downloaded and removed from the server.

Can I somehow upload those emails back up to the server?
With a POP account you can't "send" (upload) email to the server.
As "Buscar 웃" told you, if you have another email account (with IMAP of course), you can upload emails from the first account (POP account) to a folder on the second account (IMAP account).
To do that, first you create a new folder on the IMAP account, then you select all the emails you want to "transfer", then do a right-click on the selection and select "Copy To > the folder previously created". I recommend you to copy (Copy To) emails instead of move (Move To) them, to prevent any emails’ loss if an error occurs during the transfer.