Hi Ade, I have a similar problem:

I have installed a tracker in my T� and left in the motorcycle for more than 1 week, after that the battery was drained, so I take out and went to Yamaha for a complete recharge.

After that, I was unable to ride for 1 week more, and then, had a small ride of 50km to charge a little bit.

But, the engine light is always on. I went to Yamaha again, and used the Diagnostic tool, but we didn't found any fault code.
We tried to change de battery, but still, the same error.

I came back home, and discover that, when I put the high been front light, the engine fault light go off, but when I put low been light, the light pops out again....