Here's what I've learnt about this issue from own experience and reading through many threads on this forum:
1) The primary chain on the CB500 and CB550 does not have a tensioner - therefore it will always have a bit of slack
2) In neutral, with the clutch engaged/'connected', the clutch basket and transmission is constantly accelerating and decelerating with the idle RPMs causing the rattling/knocking noise
3) Loose rivets on the clutch basket, axial play of the clutch and hardened damper rubbers on the primary shaft can add to the noise
4) A new primary chain will only provide a temporary 'cure' for the problem since it will become streched again soon
5) Running a poorly tuned bike will increase wear of the primary chain, so you should keep your motor tuned up
6) The motor should be idling around 1050rpm, not below
7) A badly worn primary chain rubs on an oil channel leading to the oil filter. If this channel is rubbed through, desaster will happen
8 ) If rattling noise disappears above 1500rpm in neutral, there's no need to worry - just keep the motor tuned up
9) While changing the primary chain, the "once you are in there" effect will appear leading to more work and money spent than planned
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So if 8 applies, just leave the motor closed and keep the it tuned up
So what can you do?
Well, give your bike a - you already kown that:
complete tune up in the order a) valves - b) cam chain - c) point gaps - d) ignition timing - e) idle mixture - f) carb synchronization - g) idle speed
The official Honda workshop manual downloadable on this site is your friend.
And of course, your bike is always thankful for an unclogged air filter and fresh oil