I just had the same wish: “Simply overwriting a json file every time i make a change to the custom fields would be super!”.
In my case I found out that the exported json-file had these [] brackets at the beginning and ending of the file and the sync-file did not.
So I just took my exported json-file and deleted the brackets in the first [ and last ] line and then it was loading.
I hope this helps somebody :).
Would be nice if the files would be identical though!