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LCLS-II will add a 4 GeV, 1 MHz, SCRF electron accelerator in the first 700 meters of the SLAC 2-mile Linac, as well as adjustable gap polarized undulators in the down-beam electron lines, to produce tunable, fully coherent X-rays in programmable bunch patterns. This facility will work in unison with the existing Linac Coherent Light Source, which uses the legacy copper cavities in the last third of the linac to deliver electrons between 2 and 17 GeV to an undulator line. The upgrade plan includes new beam lines, five stages of state of the art collimation that shall clean the high-power beam well up-beam of the radio-sensitive undulators, and new electron and photon beam dumps. This paper describes the challenges encountered to define efficient measures to protect machine, personnel, public and the environment from the potentially destructive power of the beam, while maximizing the reuse of existing components and infrastructure, and allowing for complex operational modes.