Fredo made a good point some time ago that the problem (assuming yours is the same as mine was) is that some video editors aren’t consistent in clip and track management. In other words they don’t lay stereo elements in consistently over tracks, meaning sometimes music is on tracks 9/10, and sometimes 10/11. In addition to that their editing can be inconsistent so that Nuendo refuses to properly convert since the edits don’t match.
My solution, or suggestion rather, was for us to be able to tell Nuendo to force conversion regardless of possible errors, although possible by also writing a log of mismatches as they occur. But of course that’s of no help to you now since that doesn’t exist.
So Fredo’s solution was essentially “deal with it” or “get them to do their job properly”. The latter better than the first, but both are annoying of course, especially since editors can be super-hard to work with (although they have their own issues to deal with, to be fair).
The only thing I’d add that could maybe help, is to try to convert a group of tracks at a time, say 8 tracks of stereo content, and then narrow it down as you get errors. So if the 8 don’t convert, select 4. If that doesn’t work then 2. Hopefully by doing it that way you can narrow down which tracks have problems. Then once you know which have a problem you repeat the process but ‘horizontally’, by copying half of the timeline to two new tracks. Try to convert. If it works, then the other half shouldn’t work. If it doesn’t, cut that in half, and so on, until you find the offending events where edits weren’t done properly.
Only other thing I can think of is some sort of logical editor workflow, or possibly macro, which forces standardized edits/fades onto both channels. That’ll effectively undo any good work video editors did of course, but at least you can convert it all in one shot after (assuming it works).