Of course they will be wasted in the scenario the OP mentions. If he currently has 59,500 Club Miles, a 600 mile flight and a 8,000 mile flight then if the 600 mile flight posts first then everything's fine, the membership year is reset and the 8,000 mile flight posts as the first flight in the new year as a Gold. But if the 8,000 mile flight posts first, then in his new membership year as a Gold he will only have 600 miles.

The solution, as many people mentioned (before the OP rejigged his plans), is to simply delete the MPC number from the 8000 mile flight and claim missing miles later.