Just went through my chain case on 2000 Yamaha with 13,000 miles on it. Chain was so stretched it had no more adjustment.
New chain same gears. Know what you are referring to about the chain marks in the gears. Run them and don't give it a second thought.
What can it cause to go wrong? Nothing if you ask me. Maybe shorten the life of the chain by 1%
At around 7000 miles in the same chain case I had the bolt on the lower gear break. The head snapped off and made some real interesting marking in the case. Did not break or crack it so I reused that also. Same gears also. The chain was done in this fiasco.
Note :This sled is ridden harder than most.