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I recently did an oil change on my '06 R6 (~35k miles). 10w-40 fully synthetic Motul (the oil I always use) with K&N air filter. The oil level is within spec, nothing I haven't done before.
This time, I decided to clean/lube my chain while the oil was draining (2 birds with 1 stone). The bike was in neutral and the rear wheel was able to move freely. (Is this an issue if the bike is in neutral?)
Finish the oil change, put everything back together and the bike locks me between 2 & 3 (might've been 3 & 4, unsure but no neutral between the two).
The shift lever moves up and down, but will only shift between the two gears. For instance, if I am in 2nd and try to downshift, the lever moves but doesn't engage the trans. Same story if I am in 3rd and try to upshift.
Took the shift arm and lever off, sprayed everything down (lever bolt, arm links) with wd-40, and made sure these parts were able to move freely. The bike felt great for about 4 miles and now a similar problem is happening again.
Now, the bike will sometimes shift fine, but occasionally it won't upshift from 1 to 2, or won't downshift from 2 to 1. Instead, I get a dead feeling in the shift lever where it moves but doesn't shift (no clicks, no resistance).
I've heard a lot of talk about a "detent spring," could this be the cause of my issue or does it sound like something different? Is the shift lever simply not resetting properly?
 

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YZFR6... ooodles of HP
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The detent spring catches the shift drum with the stopper pawl from over travelling past the next gear. Does the pedal snap back after the "shift"? If not the return spring would be the first suspect. Find neutral by rolling tire back and forth. Then rolling try to go through the gears. With a foot or so each direction the dogs should mesh with minimal clunk or foot pressure.
 

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Discussion Starter #3
The detent spring catches the shift drum with the stopper pawl from over travelling past the next gear. Does the pedal snap back after the "shift"? If not the return spring would be the first suspect. Find neutral by rolling tire back and forth. Then rolling try to go through the gears. With a foot or so each direction the dogs should mesh with minimal clunk or foot pressure.
Okay I will have to look into this when I get home. I did notice earlier, if I manually reset the shift lever it will shift fine. For instance, if I shift 1-2, it won't let me go up from 2-3 (lever will move upwards but no shift) until I press slightly down on the shift lever - then it will shift up to 3rd. I've been careful not to grind any gears, but I've accidentally gone into neutral a few times with the clutch out. 😬
 

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So are you trying to ride the bike or shift it through the gears as it sits without moving?
If you're trying to shift it without the rear wheel rolling it is normal. It's because a motorcycle transmission is a sequential transmission. It can be shifted up or down without a clutch. But the rear wheel has to be spinning to shift with this type of transmission.
Nature of the beast.
Works different than a car. Although sometimes a car can get stuck between gears. Then you have to let it roll a little bit.

And if you are riding it and it's not shifting I'll go out on a limb and bet you don't have the clutch lever adjusted correctly. Watch the video.

 

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you probably should use a quality filter like hiflo or OEM. Not K&N. Total junk

pay attention to the knuckle orientation... there is a specific alignment dot.
 
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