The problem of partial updates without rewriting a whole large file is old, and has been solved.many times. Some old, widely known examples: zip files, also wad and pk files from iD Software games. Any of the approaches could have solved the problem of efficient updaters while protecting against a short read. (Or serve as a warning, if we look at the history of zip files.)

One of the lessons I received while growing as a software engineer is to assess if I could be the first person ever encountering a particular problem. Most often I am not, so existing solutions can be found and are worth looking at, and maybe directly reusing.