I'm not surprised about your problems with the darker levels. The i1d3 is only accurate down to 0.1 nits - reference on Tedd's page >here<. I'm struggling to find any kind of spec for your version of that meter (the i1display pro), but surely if they had improved the near-black performance they would have mentioned it at least somewhere, any not need 10 minutes of intensive googling to find nothing about it!the grayscale would take about 35 mins and it was not reading the darker levels right at all. I know it should be a easy fix hopefully especially if HDR and DV were calibrated alright.
So no, it is certainly not an "easy fix hopefully", sorry.
For this reason, one strategy that many of us find successful is to never ever touch the factory 1DLUTs, because any replacement you can create will not be as good.