But it's not the right way I guess because it generate new ones.
It's the right way, because it's the only one, which give at the SAME time: increased ground quality, compatibility with FSX without redoing the scenery from scratch for FS9 (there would be no FS9 scenery to begin with, in this case)
Why? The way to solve this problem was to eliminate the displaced threshold in the AFCAD (which btw. is not the updated AFCAD of Harpsi anymore, that contained all the updates we made like corrected taxiways, gates and the double Holding-Point bars...).
We'll integrate his fixes in our AFCAD anyway.
The right way to fix this problem of the double visible displaced threshold markings would be, to delete the displaced threshold markings of the scenery (lsgg.bgl), but only the markings, not the appr-lights! Then move the threshold-bar in the AFCAD to the right position. Please take a look on this again.
Don't you think that we did the fix the way it has been done, it's because we ALREADY tried what your are suggesting, and this obviously didn't work ? The threshold markings in lsgg.bgl are ALREADY flagged as not visible. However, it appears that FS9 doesn't honor this flag, and if there is a threshold of any lenght, it will always displays the markings, regardless if the visibility flag is set to 0, like in fact it is.
If you download the AFCAD again (from the Hotfixes), I restored the threshold as it was, but also added the latest taxiway/parking layout from Harpsi's AFCAD.
However, the double threshold markings are now back, SLIGHTLY visible, but it's either this, or the other way. As I've said, since FS9 simply ignore the 0 to the theshold markings parameter, it doesn't look to be possible to get rid of those markings. And, deleting the threshold in the background runway, wouldn't work as well, because it would affect the runway lights.