In my opinion your builder is incorrect. The notch in the rafters was simply overcut leaving the lower area without any support. There are a couple options that may be considered as opposed to removal and replacement. Purlins could be installed to accept the load of the span or the rafters could be sistered. In either case I would recommend the owners consult with an engineer and the engineers recommendations followed.
There is no way that a rafter can rest on nothing and be called supportive. I did see the shims but did not see any nailings securing the upper section that continous on. That will have to be addressed as well if that section is to remain as is to secure the rafter to the plate.

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