My Neo 5 NVME kit also came with these two cables. The documentation says nothing about two cables.
I went with the V2 cable only because 2 sounds newer than 1.3.
And I had a big problem: When I put the Neo 5 lid on, the NVME drive would lose connection to the RPi 5. No lid, no problem.
I removed the V2 cable and put in the V1.3 cable, and put the lid on. So far so good for the last nine hours. I’ll comment if the problem occurs again.
The lid has a tab near the flex cable. Instructions are not super clear, but there appears to be a hole in the non-lid part of the case the we’re supposed to route the flex cable through. When I route the flex cable through this hole, the lid’s tab presses on the the flex cable.
I considered avoiding the cable hole and routing the cable closer to the Pi board. But that would require a sharper bend in the cable, so I didn’t want to try it.
I wonder if this issue – the lid tab pressing on the flex cable – explains problems other users are having with their NVME drive.