The JSON files can exist and be used without them being synced. The JSON files are always used instead of the DB except when editing a field group, they must be synced before editing or you’ll loose chances in the JSON file that were not synced. There really is no reason to sync them if you never edit them on the production server.
You can actually delete all of the field groups on the production site and then upload the acf-json files. Deleting them from the site will delete them from the acf-json folder so you need to upload them.
If you want you can set the JSON files to private, they will not appear and you cannot sync them if you do this. This is explained near the bottom of this page https://www.advancedcustomfields.com/resources/synchronized-json/
