Yes, you can’t delete a flag (even a custom one) once it’s been used as you need the data for historical reasons so it doesn’t break the review queue.
Disabling one will remove it from the flag menu and leave only the enabled ones as ‘live’ flag options for your community to make use of. 
Though as you’re looking for an option where staff can discuss flags you may want to consider Moin’s idea. It may suit your site to ask for more details on every flag, but if that’s not the main intention then the flipside to consider is that it adds more effort/friction for the user flagging a post (which may lead to them giving up before reporting something)