Will there be naming conflicts if I upgrade my contracts on Daml on Fabric (or any ledger)?

Are you running the json-api separately with the daml json-api command? You’d do something like the below to connect your json-api to the ledger api (via the ledger flags below) which would give an endpoint that Daml Script could use in json-api mode.

daml json-api --ledger-host localhost --ledger-port 6865 --address --http-port 7575

But if you’re able to just have Daml Scripts talk to the Ledger API then no need to have the JSON API in between.