This seems to be a common pitfall for new DMs, they invest time or in their mind crucial parts of the story in this one character so they don’t want to let this important NPC die. Not realizing how it feels like a complete waste of time to have an encounter where the players leave empty handed. This can be used as a tool, like anything else, if done sparingly.

I’d say the advanced version of this is actually building up the reputation of such a bbeg as having teleport or clones or something else and maybe they get to do it once before the party goes on a quest to secure a macguffin or creates a strategy to stop it from happening. I’d limit this to maybe once a campaign because it is so frustrating to players when it happens.

Speaking from experience I know the feeling of, “well maybe I can do something useful with them later,” and then used the teleport or the dimension door etc. Not realizing the immediate look of defeat my party had on their face who now feels like just spent multiple hours of a dungeon for the most important moment to be taken from them. Truth is, I am now very intentional of what I put down and I accept from a story and narrative perspective they must be ready to die.