If you run the installer and pick the add/remove scenery option, it will highlight the area on the map you have only partial files for, and if you continue the install it will replace anything that's missing. If you have partial files for a highlighted area and deselect it, so it's no longer highlighted, the installer will remove any files you had.
So the installer can still work with partial installs, but will only try to match your selections on the map in full.