Flagged emails are not deleted by default
Flagged emails may play an important role for a user. There can be tasks, deadlines or workflows linked to a flagged email. To not impede these workflows, flagged emails are not deleted by default. Emails marked as completed are an exception and will be deleted if there is a deletion rule covering that email.
Flagged emails will be archived, unless there is a filter excluding the email otherwise. In case the flag of an already archived email is removed in the mailbox, the email may get deleted if there is an deletion rule covering that email.
How to delete flagged emails?
The option must be explicitly activated. For archiving profiles accessing Microsoft Exchange or Microsoft 365 servers, the option is called Also delete messages marked for follow-up, while for archiving profiles that access the email server via the IMAP protocol, this option is called Also delete flagged messages.