If it were a domestic EICR you would not isolate and leave off a C2 circuit (which from BPG #4 applies to high Zs), rather you would report the issue and the landlord has 28 days to have it fixed. C1 is a different matter, then you would not restore power as it presents an immediate danger.
So the real question to me is how serious is the high Zs case?
In an industrial environment the risks from high Zs could be less than domestic (if controlled environment, skilled staff, etc), or it could be so much higher it really merits a C1 danger category - in which case you would not re-energise.
That is where you need to apply some judgment and to report the nature of the fault in such a manner that the person in charge can make a sensible decision about the time-scale for remedial action and the impact of down-time.
High Zs could be due to a fault, in which case (a) it might get worse and (b) that could become a hot-spot / fire-risk in the event of a fault. However, from what you said it seems the Zs values are probably the result of poor or no design / measurement in the past.
Whatever the cause of the high Zs values, the impact is the same: longer (or in the worst case no) disconnection times. That in turn presents a higher risk of shock from the touch potential of earthed metalwork involved in the fault, and it also poses a risk of cable damage or even a fire if the resulting I2t exceeds the cable's adiabatic limits.
The risk of shock is also dependent on what is involved, If it is machinery that is on its own in a dry area then probably a low risk of a serious shock current-time exposure, where as external metalwork like street lights could allow someone to have a very serious shock.
Similarly the adiabatic risk depends on several factors. Generally if the OCPD is able to overload-protect the cable, and the CPC is the same size, then you don't have any fire risk. However, if the OCPD was intended for only fault protection, or if a reduced size CPC is in use, then it merits a far more serious check. Then of course the environment is also a factor. Cable in metal conduit is not likely to start a fire, but flex in an environment with other combustible materials, solvent vapour, etc., is quite a different matter.
If you have your measured Zs and it appears to match "poor/no design" as the reason, then I would plug it in to the time-current curve of the OCPD and get an idea of the range of disconnection times and look at quite what that means in practice, and also if there is any RCD (even a delay incomer) that would also provide ADS, to get an upper I2t value and see what it implies. If on nominal volts at the site (not the Umin of the regs) you see over 5s then I would worry.
This rambling discussion is not really answering your important question about what to do in a simple way, but in practice you often have to deal with imperfect systems and trying to inform those above of the severity of a given non-compliance is important, and also if you believe there are low-disruption fixes possible (e.g. running another CPC in parallel / supplementary bond to reduce R2 enough to meet the regs, maybe going for a lower MCB rating or D->C->B curve if it is not absolutely needed for the load in question's inrush characteristics, etc.)