There are a number of factors here, from game system to campaign style. If you have long term story hooks that involve the character, that's probably something you should discuss with the player. There may be a chance to salvage the existing character, or bring back the original, if you are able to work with them to make changes to their power set, or some other aspect of the character.
With that in mind, I think part of this comes back to session 0, and expressing the format of the campaign. For my personal games, I don't have an issue with players character swapping, and in a super team, it's kind of expected as rarely do you see every here "on screen" at the same time, so I like to set up rotating conditions to bring heroes in and out. As I mentioned before, if we need a specific character for a part of the larger campaign, I'll let the player know that we want to spotlight this character and they can swap later.
Sorry for the plug, but it relates to the conversation. The Metahumans Rising core book talks to these concepts for a session 0, people running multiple characters, one at a time, and swapping them in and out between stories.