I've removed the main engine case on the right hand side of my 3en2 (to get it powdered or chromed etc so it looks better next to my other ally covers). It's the one with the oil filler cap and the Yamaha logo on it.

I found that on the inside of this case/cover, there is a metal plate bolted to four mounting holes, with a rubber damper behind it. - Can anyone tell me what this is for? can I just do away with it?

I've had to drill out one of the screws that holds this plate on to remove it and I've made a right mess of the mounting point (I've drilled it off center). I'll probably have to clean it up, fill it with quick metal and re-tap it, so I can refit the plate. I'll probably pay the local metal shop to do this so I don't wreck it further, if it has to be done.

Unless I can just ditch the plate? - any suggestions, help or just pointing and laughing would be appreciated.

It will be the clutch cover you are meaning. If it is then just but another one off ebay, they don't make big money.
My 3tj has exactly the same thing inside the clutch cover, but luckly my bolts came out ok.

I don't really know why it is there. It could be to stop vibration or it could be there to stop fragments of exploding clutch from going straight through the casing into the riders leg if the clutch were to let go in a spectacular fashion.

It is just a noise / vibration damping device. There is a similar one on the sprocket cover, which can be removed with no issues - other than checking the torque of the fixings occasionally if vibrations are higher.

The purpose is to change the resonant frequency of the covers to reduce noise throughout the rev range.

Cheers Bob, so the long and the short of it is that I can lob it and not worry that much!