Having removed the front head light sub frame ( to straighten the wing mirror bracket arm) I noticed that
that some of the wires from the fuse box have been cut

and also one wire going to the indicators


Bike starts, runs fine (now ) lights work and the indicators flash,

anybody know what they were for?

Gaytime Running Lights, only in Japan they are amber

Correct. The white / blue, orange / white are for the indicators.

If you havnt had them out yet there 21/5w dual filament bulbs, they act as running(side) lights when wired up but dont meet uk specs so people remove them