First, AMD Warranty doesn't cover bent or broken pins or Customer error (Processor damaged when removing CPU Cooler).
Second: if the scratches are very superficial and not deep at the bottom of the processor, in my opinion, I don't believe it will affect anything. But if the scratches were on the TOP (the Heat Spreader surface) of the processor, it could prevent proper heat from being transferred to the CPU Cooler or heat sink thus causing it to Overheat.
Third if the processor is working normally when installed then, again in my opinion, it should be fine. Make sure it isn't overheating and the computer is working normally. You can always run a CPU Stress test to make sure it is stable with those minor scratches on the bottom.