That explains a lot. ACF will not delete entire field groups if they are missing from the acf-json folder. What you are seeing is expected behavior. ACF will only save changes, load groups, and sync groups that exist in the folder.
I you want to automatically delete groups, I’m sure it would be possible, but you’d need to right custom code to detect the missing files and tell ACF to delete them. I don’t know of any examples of doing this or the code that would be involved, but basically you’d need to get a list of all the groups and see if there is a corresponding json file and if not then tell ACF to delete the group.
