This post from November reported a problem of supposed duplicate names across the Legacy folder and the PBR folder, and in that regard, my reply back then was correct, because at no time these two folders are both active in P3D4, and even if one of them is there, and empty, is NOT added and NOT seen by simulator, since the Legacy folder path is NOT included to the add-on.xml that is active in P3D4. Only the add-on.xml for P3D 3 or the FSX.CFG in FSX will use it.
The OP reported SimDirector flagged as duplicates two objects with the same name, one in the PBR folder and another one in the Legacy folder, and this is NOT a case of duplicate files, and if SimDirectory was really reporting *that* (I had no reasons to doubt that user report), it's clearly a mistake, because the Legacy folder is not registered to P3D4.
However, this was in November, and you are now reporting a totally different thing, which is duplicate names inside the same main folder, so I checked, and yes, there are some, and it will be obviously fixed in the next Live Update, since ( as usual ), each and every problem reported is always fixed, when it's our to fix.