This happens quite often, if it's a minor change/addition on a large site, it frequently isn't possible to shut the whole site down.
When I review the certificates etc that get passed to me, I compare the Zs along with R1+R2.
So for example, the allowed Zs is 1.1 ohm based on the mcb/rcbo and the measured is 0.5 ohm, with R1+R2 of 0.4 .
In this case the Ze is around 0.1 ohm, even if this was to double/treble/quadruple by removing the parallel earth paths, its still well within the 1.1 ohm - so the whole situation is clearly safe, even if we don't have actual values for Ze.
However, if this same circuit had measured Zs of 1.0 ohm, R1+R2 of 0.2 ohm this would give a Ze of 0.8 ohm, any change in this due to the removal of parallel paths could easily result in Zs going above the allowed value.
In this case, I would look to get further tests as I couldn’t guarantee that its safe as it is. This would be finding the parallel paths, for example the board feeding this board, may have no parallel earth paths, and may itself have a R1+R2 of say 0.6 ohm, so the likely Ze is more in the order of 0.2 ohm this would still be an issue in this case as only a 50% increase in value due to removing parallels would hit the limit.
It is normal therefore to use Zs at the board to be regarded as the Ze on the form (in fact ammendment 2 on the 18th suggests this clarity on the form), and only really require further investigation if the values are close to the limits