What Jeff said, basic stuff first. Then I would start to look at possible thermal issues causing vapor lock in the fuel system. Does it run OK hot before you shut it down?
I'm not familiar with the Mag Marrelli EFI and firmware, but my Cannondale had on Optimum system that incorporated a max temp limit for the engine. If this was reached the ECU would shut down and not allow a restart. Does the GasGas include such a safeguard? If so, and your bike runs very hot, the high temp spike when shut down may keep it from restarting. Just a thought.
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