2003 warrior l200 and when braking you could hear a whirring noise from underneath and then a thud, the green 4 wheel drive light then started flashing but wasn't in 4 wheel drive, it doesn't do it all the time, just when heavy braking.

Started it up later and the light had gone out?

Any ideas, on the mot there was an advisory on gearbox mount ineffective?

Gearbox mount is meant to be like that , seems fecked to death but that is it's design...
The braking issue I would say is likely to be a vacuum leak on the truck somewhere, when braking you will nick some vac from the system to operate the servo, this has starved the system of vacuum and that's why the green 4x4 light came on, I will also suggest that the front wheel drive actuator was trying to engage when this happens,, cause by the lack of vacuum..