You should never delete a contact from your MailUp console. Instead, when you want to manually remove a current subscriber from a list, edit the user (the pencil icon) and set his/her status as "DISABLED". This way the user will be moved to the UNSUBSCRIBERS list (i.e. OPTOUT) and will no longer receive any further communication from you.
In the event of new imports, if the user has been previously disabled he/she will not be imported (unless you want to, in which case you will use the appropriate option to override existing unsubscribers' preferences).
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