What should replace intra-file license headers in source files in judrisdictions which necessitate it?

Are you sure this is a real problem?

Your example of json is easy, just add an extra property at the top.

But I would do something different for a generic approach. You can change the code which loads the json, (presumably part of the same paackage) to load a different file. Put your change explanation in the top of the code file ("changed to load X.json rather than Y.json") and make a new duplicate + changes data file to load, leaving the original unchanged and unused.

You could even change the file format or loading procedure to filter out the comments.

Or add a preprocessor step on compile to remove all the comments?

So your problem is only a problem if..

1. The licence specifies you must put a comment in the changed file
2. The file you want to change is in a format which doesn't support comments
3. The files isn't a "data file" you can just replace out with an alternative

Given that licences can say anything it's not crazy to imagine a scenario where the licence accidentally prohibits a change. But in this case you could just ask for a change to the licence?

OR. I feel i have to add, given the lack of enforcement of copy-left licences, you could just ignore it and put the comment in somewhere else. Can you really imagine a court deciding against you in such a case?