Personally, I am not sure, and I haven’t touched ACF in months due to I am no longer developing 🙂
When you do a manual sync does the process remove fields that have been removed from the JSON file? If not, then there’s probably a reason for it. 99% of the time developers allow the addition of data like this through imports, but not removal of the data. This is due to it is much easier to have users manually delete data then try to recover any data deleted from the database due to a bad import.
