I have heard of some owners repainting the cases themselves.There is a thread on Multistrada.net somewhere.
You can get some silver heat resisting paint and laquer from good car supply shops that will do the job.
Depending on the affected area,its gotta be easier with the motor out of the frame.Then there is all the wiring/plumbing/brackets to mask/remove...........hmm,a big job I think.
When the problem first arose on my bike,Italia said they have a guy that airbrushes the new paint on.(It was then just a small area of flakey paint)It was when the motor was lifted out of the frame they found out the full extent of the damage.
The painter said no way could he do anything with that.