If you want him to operate as SIC under Part 91, then it's a non-issue. There is no SOP. He must be familiar with the aircraft and make three takeoffs and landings, per 61.55. If He's type rated in the airplane and wants to act as PIC under 61.58, then he only needs a check in type every 24 months, and a a check every 12 months in any aircraft certificated for more than one crewmember.
No specific training program, no SOP.
61.55(d) specifically excludes Part 135. So does 61.58(b). In other words, neither of those subparagraphs apply to operations conducted under Part 135. If you want to conduct operations under Part 135, you either need to use your approved training vendor (as provided in your OpSpecs A031), or have an approved training manual and program to meet the qualification requirements under this part.
Under Part 91, you need no such program.
I'm not certain I understand your question, then. Is this man dequalled because he is out of his six month check to act as PIC under Part 135? If that's the case he's good to go under Part 91...he only needs a 12 month check in any aircraft requiring more than one crewmember. He only needs a 24 month check in type. Just how far out of currency is this individual? If he's more than 12 months out for 61.58, then he's certainly at least 6 months overdue for a PIC check under Part 135.
What exactly is the story, here?