Flagging the emails will not prevent them from being deleted after a period of time.

What does flagging an email do?

You can flag an email message you receive to remind yourself to follow-‐up or take action at a later time. Your flagged message will appear in the To-‐Do Bar, in Tasks, and in the Daily Task List in Calendar. You can also click your Search Folder – For Follow Up to find the messages you've flagged.

Do flagged emails get deleted?

Answer: 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 never deleted by MailStore. ... However, flagged emails will be archived, unless there is a filter excluding the email otherwise.