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
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