If the transmission is starting to go, flushing the fluid can be a BAD BAD BAD thing. ATF contains detergents and other pretty strong chemicals that can actually finalize a dying trans. When I worked at AAMCO we were not allowed by corporate policy to change the fluid on any car if it had a burnt smell or looked even slightly brown. If the clutch disks are starting to burn up, the detergents can actually speed up that process and cause the unit to fail very rapidly. Valvoline has issued the same policy since they got stuck with numerous rebuild bills from flushing the fluid on cars that were very close to death.