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That Torx head bolt is the centering pin to adjust the shifter pawl. You can remove the bolt, apply some Loctite thread sealant with PTFE and reinstall the bolt. Sometimes the bolt will bottom out before interfering with the shifter pawl/drum; sometimes not. The bolt should be threaded in as far as possible without interfering with either.
The centering pin is used to adjust the shifter pawl. You want the shifter mechanism to move the same amount back and forth, whether you are downshifting or up shifting. It is best to remove the top cover to watch the adjustment but if you can manually shift through all the gears (rotate rear wheel and shifting up and down), you wan't have to to that.
Can the bolt even come out without removing inner primary?
I would try black touch up paint, shoe polish or a sharpie before I did anything else.
Brings me to these points;
1) from where I sit on my motorcycle, I would never be able to see that bolt.
2) when my bike is out of the garage, it is being ridden so likely nobody else will notice that imperfection.
3) who cares about 1 rust covered bolt?
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