I had a little adventure with LOD2, back at the start of modding...
I had made LOD1 with around 13k triangles and copied them all to LOD2, switched to LOD2 view and started attacking it. I figured that I'd keep any edges as they were to keep the shadow profile smooth, and just remove all the detail from the flat parts as that couldn't ever affect the shadow. I spent about a day of work over a week, I think, carefully choreographing the order of endless "merge to green" operations. (you can see where this is going now
)
It never occurred to me that the points in LOD2 were the same points as LOD1 - it was quite a shock to see LOD1 mangled flat when I finally switched back, lots of swearing
(no blame btw, it's the sort of thing I should have a) checked and b) twigged from the fact that there were also points there for triangles that I hadn't copied).
It also didn't occur to me that I could save what I'd done as a separate object and just import it into the last unmangled backup I had... so, I'm currently doing it again that way. This time around I have the "reduce detail" tool, so it's not so bad as the first time
I don't know if it's worth separating the points for LODs, but I can definitely vouch for it catching out people who aren't paying proper attention. Maybe a text warning when you're merging points or using reducing detail in any LOD other than LOD1 might be enough.