First of all, the JSON file of a doctype define the fields configuration of that doctype?
In ERPNext, I have a custom Doctype in Manufacturing Module. I modified the JSON file to configure the fields of Doctype, but the changes does not effect in Doctype after execute the following commands:
bench clear-cache && bench update --build && bench migrate && bench restart
The configuration in the Doctype is the one I made directly on the Doctype.