Anyone looking for the answer, this post helped: https://awesomeacf.com/understanding-where-your-acf-field-group-settings-are-coming-from/
Apparently the .json files produced from acf-json don’t sync all of the fields directly to the database as I expected, ACF will automatically read the fields from the .json file each time a backend page is loaded.
To fix, I deleted all ACF fields from my database, ensured I didn’t sync anything using ACF’s sync option on dev / production, then simply uploaded the acf-json folder to my theme directory. The fields showed as expected.
