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Hi Yuan,
Yes, if you have different levels of demand (say, for electricity) for different scenarios, then the amount of electricity that will need to come from the Transformation module will differ, as long as you have sufficient generation capacity.
When you view Results for the Transmission and Distribution branches, by fuel and scenario, as you mentioned, you're not only looking at the losses that you entered in the Analysis view; you're looking at the total output (by fuel, of course) which is affected by many of the other values you enter in your scenarios.
I still feel like I haven't quite grasped your question. If this is still unsatisfactory, maybe you could send me a screenshot, or your data set, describing the problem to leap@sei-us.org.
Hope this helps,
Taylor