I'm not with Laminar Research, just a fellow simmer in the UK, but I have a couple of questions:-
1. For the scenery that is 'missing' (gone), is it X-Plane 11 default scenery or an addon scenery package?
2. Are the 'deleted' scenery folders, still deleted now or have you managed to recover them through the X-Plane Installer app?
3. Please could you upload your C:\X-Plane 11\Custom Scenery\scenery_packs.ini file for others more knowledgeable than myself can assess it?