Key Fob Duplication after Wiring Loom Swap

I have a 1996 Defender 110 with a passive immobilizer. The OEM key and fob work fine. Problem is, I only have one fob. I went into a Land Rover specialist to have a second fob made. No problem there. As they were about to start, a tech that worked on my Landy previously told them the duplicate wouldn't work because of the wiring loom replacement they had done the month before (the old wiring had melted and shop had to source and fit a second hand loom. But there was some compromise in the replacement that apparently made it impossible to use the regular fob programming/reprogramming possible).

Anyway, my question is basically this: Is there some ninja locksmith out there who can simply clone my existing fob so I have a back-up if my working one gets lost or damaged? Or is that simply impossible the way the passive immobilizer system is engineered?