First guess: you modified both Permissions and Granted lists? After which Permissions does not match what .desktop has → looks like application requirements have changed → ask from user again. It should work if you: stop the service, edit just the Granted list, restart the service.
While the settings UI etc is still missing things, the underlying interfaces are already there, e.g.
$ devel-su
# dbus-send --system --print-reply --type=method_call --dest=org.sailfishos.sailjaild1 /org/sailfishos/sailjaild1 org.sailfishos.sailjaild1.GetGrantedPermissions uint32:100000 string:sailfish-office
array [
string "UserDirs"
string "MediaIndexing"
string "RemovableMedia"
]
# dbus-send --system --print-reply --type=method_call --dest=org.sailfishos.sailjaild1 /org/sailfishos/sailjaild1 org.sailfishos.sailjaild1.SetGrantedPermissions uint32:100000 string:sailfish-office array:string:UserDirs,MediaIndexing
# dbus-send --system --print-reply --type=method_call --dest=org.sailfishos.sailjaild1 /org/sailfishos/sailjaild1 org.sailfishos.sailjaild1.GetGrantedPermissions uint32:100000 string:sailfish-office
array [
string "UserDirs"
string "MediaIndexing"
]