See that's a shortcoming with EF Core and model creation is that if you have any customization in the DbContext, you'll lose it all if you Scaffold the DBcontext again based on new changes, and the DBContext being used by the program is overwritten by the new DBcontext.
What do you do what do you do to prevent DBContext customization from being lost in this situation?
I have resorted to Scaffolding the output of the Dbcontext to a staging folder in the VS project and done a copy/past operation of what's new in the new dbcontext over to the current DBContext being used by the program.
What other choice do you have?
If you don't have customization in the DBcontext, then by all means, just overwrite the DbContext.cs used by the existing project.
If your Dbcontext is huge, then you could Scaffold output to the staging folder and do a file comparison between the current and new DBContext(s), note the changes and copy/paste code appropriately. Visual Stuido has a file comparison feature you can use.
https://www.meziantou.net/comparing-files-using-visual-studio-code.htm