Flutter is caused by the SPEED of the air molecules over the control surface not the number of molecules. So yes, Vne decreases with altitude, but as Peter points out, in your design configuration you won't be anywhere near those speed in normal operations.
The problem comes if you boy race your aeroplane, bung in an extra 200 HP with turbo and super charger, so now you can cruise at IAS-Vne at 30,000'. You will actually be over Vne-TAS.
Vans has a very good article on this on their website.