FlyAgi

I strongly recommend not to micromanage the scenery order. This is completely unnessessary and just causes additional work. Make sure that all mesh sceneries are placed at the bottom of the file (in the right order if you have different meshes for the same location of course) and below global airports. All custom airports have to be above global airports and libraries can be irgnored for most part - if this is all true, most of the stuff will be fine.

Well... that sounds like a somehow broken scenery order. What does not show up? TrueEarth or the global airports? If TrueEarth does not show up you will very likely have some other mesh sceneries placed on top of it - make sure that TrueEarth is above ALL mesh sceneries and below global airports.

It's not that hard. Regarding TE-GBS all you need is to care for the Global Airports entry and then place all TE-GBS entries below the Global Airports line, in the correct order, A, B and C. Of course you will need to do this manually in the scenery-packs.ini file. If you are looking for a scenery organizer you should try xOrganizer.

Your method works by deleting the entire scenery-packs.ini and let X-Plane create a new one by alphabetical order. The JV method has to be done manually, you have to edit the scenery-packs.ini and move the entries to the right position yourself.