Is manualy updating JWT access_token data considered a bad practice?
It seems like you're trying to use the JWT as a session storage mechanism, which is not a good practice. If you need to check the validity of the JWT in the database on every request why not just use sessions and keep the relevant data server side?
Also, how do you plan to deliver such an updated token to the user? I think that it will be much easier for you to keep the data in the backend and just use sessions.