If I move E-Mails to archive in apple mail will they still also be on the server?
Or will they only be on my computer then where the archive is?
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If you use a email server that uses the IMAP protocol or Exchange all your emails and folders will be saved on the server.
iCloud.com, Gmail.com, Outlook.com use either exchange or IMAP. If you have your own email server, you should connect to it through IMAP.
IMAP was designed with the goal of permitting complete management of an email box by multiple email clients, therefore clients generally leave messages on the server until the user explicitly deletes them.