mail flagged file

I have old flagged emails stored in designated folders and consequently have close to a thousand 'flagged emails' in the 'Flagged' file. Does that file eat space as an 'active file' like Inbox, Sent, Trash therefore slowing me down? If I delete items from Flagged File' it seems I delete them also in their 'resident' folders so I just keep building a larger "Flagged File"???