Didn’t read through the whole thread but …
Please do not compare the two dialogs as shown in the OP. The first one shows what is in the database after de-duplication as well as resolving of add-ons and the second one shows what was Found while reading the library.
From the manual, chapter 43. Load Scenery Library:
The final number of airports, navaids and other objects shown in the
Load Scenery Librarydialog are lower than the counts shown in the progress dialog. After the data has been loaded, a separate process removes duplicates and deletes stock airports that were replaced by add-ons.
The more add-ons (especially the Navigraph update) you have the more differences you’ll see.
I just ran my current development version with scenery library from 1.16.2 and an older scenery library and see no big differences. Left side is new (1.16.2) and right is an older scenery library. Navigraph update excluded.
What you definitely will see is missing approach procedures since the internal structures have changed. This will be fixed with the next LNM update which will also bring SID and STAR.
BTW: Latest is 2.6.11 which is also shown in the main window title bar.
Alex