Just reiterate Do NOT install P3D v2.5 AND ORBX software. ORBX has posts that Lockeed Martin's new v2.5 has major problems with ORBX scenery installation. Wait until ORBX has worked out the problems with LM. ORBX will announce when things are working again.
Well some of us like to piddle especially since we can always reload everything...lol. I didn't uninstall anything on my setup except 2.4 and left everything else intact. I did back up my terrain and scenery config files before doing so. I thought I had the issue solved until I looked at the large water bodies in the sim. They were all wooded areas. So that told me the issue was a terrain configuration one.
LM moved the terrain.cfg file out of the main P3D folder to a ProgramData\Lockheed Martin\Prepar3D v2\ folder. I copied the terrain.cfg file over to that location and now I see everything in the right perspective.
Pretty sure the 2 areas Orbx is working on fixing is "object flow" and the installers "FTX Central". The current FTX Central applications update the terrain.cfg file in the old location. I will assume copying the terrain.cfg file over the the Program Data location after applying all your regions would do the trick.
In other words, place a copy of the terrain.cfg in Program Data in the old location. Do your updates/installs, the copy the terrain.cfg file back to Program Data.
I may be off base, but it works for me.