Shortening Roof Rafters for Flat Roof Addition
Typically what is done  is the main roof is left intact and the shed roof rafters are set to a ledger that is set on top of the main rafters. That will mean a long angled cut on the shed roof rafter which, according to your drawing, by the time the angled cut it set to the ledgers the bottom corner so to speak of the shed roof rafters will be very close to the bearing wall below. The ledger may need to be done in two runs to cover the whole cut of the shed rafter. Or, with some layout, a single run of 2X12 set so the heel of the cut is at the lower edge of the 2X12 ledger. The rest of the rafter will set directly to the roof sheathing which can be applied before any of the ledgers are set. Just be sure that ventilation will flow from one roof to the other so heat does not build up with no place to go.