I suggest you enter the wall loss as corrosion in CAESAR II and set the configuration to "All Cases Corroded". In this way, your loads will be based on full wall but all denominators in stress calculations will reflect the current, corroded thickness.

Keep in mind that B31.3 is a "new design" code. Para. 300(c)(2) says: "This Code is not intended to apply to the operation, examination, inspection, testing, maintenance, or repair of piping that has been placed in service."