Hi Laitch,
It's all back togeteher again now, looks like I got the shim from the old part and the replacement mixed up. They look identical, though having now learned the importance of the thickness, I measured them both and it turns out there's a 0.2mm difference. I disovered another method of testing the preload, the "drag method'. I thought that the drive should just spin free but apparently there should be 1.1-1.8NM drag. Once I put the right shim back there was some resistance when I tried to turn it, but not too much. Now it's back together and there's no knock. I'll call into my local bike shop and get them to test it properly later this week as I don't have a torque meter that can measure that low.
Also, I must apologise. I discovered that it is indeed a flange nut on the bearing.

IMG_1721.jpeg (40.69 kB . 768x526 - viewed 78 times)I'm guessing they've added this because the new bearing doesn't come with a pre set torque, just says "don't over tighten". The original pins had to be torqued to 150 and 105Nm. I've torqued the new pins to 80Nm and marked them to show any loosening. Maybe the flange is to give a greater reistance by having a bigger surface area?