How CFS3 works or rather, what stops a feature working is somewhat of a mystery. Anyway I took TOW I and replaced most of those folders with TOW II folders, such as aircraft airfields facilities global layer Vehicles and so on, and the runway lights worked. I have yet to check TI effects. EDIT since checked and they also seem OK.
I also looked quickly at duplicates using dupeguru-win64.exe. Of course it produced a raft of files, some of which I would not classify as duplicate but am not sure. If the file name is identical, then even if it is kept only in one place, will all other cases where it is called for, find that file? I am thinking
.wav files
lots of dds files, especially in 'weather', but also in aircraft, vehicles, etc.