Mine is a mere opinion - you need his Brightness for the definitive answer.
Since the purpose of EFLI testing is to ensure that the over-current protection devices trip within a minimum (specified) time (i.e the earth loop impedence is low enough to ramp the overcurrent up quickly), and also since the testing regime says one has to test at the mains entry supply point, at EACH CU, at each socket and the proportion of the lighting circuits, its clear what testing has to be done - the annexe has to be tested in its own right - then deal with the 10mm T&E.
In the annexe, testing will be straight-forward, so I guess your question doesn't relate to that - and the maximum impedance permitted is measured back to the annexe CU.
I guess your question relates to the protection afforded by the 50A MCB at the house - whose purpose is surely only to protect from a cable fault between the 2 CUs. My guess is that you measure the EFLI between the 2 CUs - and relate it back to the maximum impedance allowed for a 50A circuit. In which case it is the impedance of the cable between the two CUS (and its connections) that you are measuring - and you don't take it into account - since it is that very impedance that would prevent the 50A breaker tripping in adequate time under a fault condition (if too high an impedance).