I wonder whether you are looking for the solution in the right direction. Is 
there theory for the shape of the curve? In that case it might be better to see 
the problem as a fitting problem.

Other than that I think option 2 is too ad hoc for scientific work. I would opt 
for simply not showing the smoothed curve where it is not available. The convol 
function you specified here is a very narrow Gaussian, is that the function you 
actually used?

Note: The code you provided can not be executed
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