Hi, sorry for the late post. I just had my R1250GS engine replaced due to this noise. I took it to BMW and said if you can't diagnose it then it's not safe to ride, I won't accept 'we don't know what it is'. I suggest you push on this! Also, put a camera/gopro on your bike to record the noise, it's MUCH easier to get it sorted if you can provide evidence.
Here is the sound my bike made, is this similar to yours? Low RPM acceleration in any gear and 70mph on the motorway.
Rattle sound video 1
Rattle sound video 2