Hi mimblgrimpf, and everyone around! First post here, so I'll take the time to thank you all for the work and information you spread in this place.
I had the same issue regarding the land disappearing once I reach an altitude of 140km. I'm running KSP 1.6.1 with Spectra 1.1.7, with PlanetShine, DistantObjectEnhancement, and KS3P.
Here's the fix I found out:
You can edit the scatterer config file for Kerbin that Spectra uses (Spectra/Spectra_scatterer/Planets/Kerbin/atmo) and tweak the skyExtinctionMultiplier on the last item (where altitude value is 140000) from 0.06 to 1. I also changed skyExtinctionTint from 1.5 to 0.5 to reduce the yellow tint on the sun's reflexion, and adjusted these values for the two previous items for continuity's sake. You can play with these values in-game from the EVE config UI and finesse them to your own liking (make sure to select the right item for your altitude).
I hope it helps!