This is one reason we strongly recommend keeping 2 installs--one for the shipping version & one for testing the beta.
The "do this for all files in this directory" only works for files within the exact same path, i.e. it would work for all the .dsf files in Global Scenery/X-Plane 11 Global Scenery/Earth nav data/ +30-010/, but you would still have to acknowledge changes in Global Scenery/X-Plane 11 Global Scenery/Earth nav data/ +30-020/ as well.