In order to update the registered CPTs, Taxonomies, Field Groups, and Options Pages from JSON files, these files need to be placed in a acf-json file in the active theme, after which a Sync tab appears in their corresponding index page and each "declaration" can be synced from the file to the WordPress database.
While this is clearly and primarily a dev tool meant for syncing changes from source control, it would still be nice to offer a more friendly UI to allow users things like batch syncing or seeing a diff-like summary of the changes.