Taking the lid off an airbox usually means that the flow of air to the carbs is less restricted. This means that there's effectively more readily available air to mix with the fuel being metered out of the various jets in the carb - the charge temp before the carb almost always drops slightly and the intake velocity can on occasion go up etc.. it all gets a bit complicated an beyond me frankly but it makes sense that the running conditions change at different throttle positions and not an arbitrary value when you mess with the airbox so you need to re-evaluate the whole carb setup.
That usually results in the mix potentially being too lean (too much air / not enuff juice) and the engine could get too hot and either sieze up from the heat / lubrication failure or if the bike it tuned, make other factors become more crittical.
Personally, I'd leave it alone and make sure the filter is clean and the carbs set up as best you can.
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