I'm a bit confused about your comments regarding the P3D library order. That order was the same as in FSX or FS9, so what was confusing about it ?
And even in XPlane 11, the order in the scenery_packs.ini is still similar (although not *exactly* the same) as FSX or P3D. Base meshes/sceneries below, more specific areas above.
I think it was maybe not necessary to reinstall everything on your sim.
Maybe you could just post the content of your scenery_packs.ini for us to take a look. The XP experts here might have a chance to spot the problems and make some recommendations
Most likely, your scenery_packs.ini got messed up because it got regenerated by the sim (no idea why), but solving the problem is just about getting the lines inside in the correct order again, I think.
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