Hmmm ok Jim. But Tongass just a straight simple install into FSX. There is no fixing of anything after install except the insertion points in ORBX Central. Most scenery files themselves don't usually get corrupted - it's the configuration files - In your case possibly the FSX terrain.cfg file got corrupt for some reason (ORBX entries can do that) from the Open landclass installs creating entries in your terrain.cfg so it could be the terrain.cfg that could be the culprit here.
1. Is ORBX Central is failing to hold your saved insertion points? You would be able to see that in your sim scenery library: check your layering from the bottom up. (your sim scenery library should match the layering pic below). (If not Check your insertion points again. Use ORBX Central Sync to sync your scenery library and re-check in your FSX scenery library. If all good, start up the sim and check a few Tongass locations).
2. If the scenery layers are in the correct order, then you have to rule out either the Tongass scenery files issue, (which I doubt) or more suspect a corrupt or lacking terrain.cfg that controls the terrain placement.
If you have the same land class issues for Tongass, then try uninstalling Tongass completely and then do a reinstall, re-setup the insertion points in ORBX Central and give it another whirl- which would hopefully fix the Tongass scenery if there was any corruption in your scenery files themselves and also possibly fix your terrain.cfg.
3. Now there is another side of this: a corrupt terrain.cfg file. This file entries control the placement of land class, water class. Orbx puts a lot in to the terrain.cfg with the FTX Global and North American Open LC entries and so does Tongass entries. So if corrupt would mess up your land/water classes.
If the same issues after the Tongass reinstall in 2. then will have to try to manually fix the terrain.cfg (which controls all of the terrain elements).
A. Try verify files for the Orbx North America LC, ORBX Global, Vector if you have them as well as ORBX Libs.
B. (The latest Orbx Central should have created a backup of your terrain.cfg (hopefully before your terrain.cfg problems).
I think your fsx terrain.cfg file should be located in folder C:\Program Files\Microsoft Games\Microsoft Flight Simulator X but if not you'll have to search for it. Anyways make a backup copy of your current terrain.cfg then use the terrain.cfg backup created by the latest orbx central and rename it to terrain.cfg. (This means whatever you installed after putting in ORBX central it may have to be reinstalled or files verified in ORBX Central as their entries might not have been present in that backup terrain.cfg. Using the old terrain.cfg: see if that fixes your Tongass. (You can always revert with the original terrain.cfg file backed up).
So a bit of troubleshooting to try to figure out the exact problem in either the layering of the scenery library, Tongass issue itself, Orbx central and/or the terrain.cfg entries. (I suspect the issue maybe in the terrain.cfg if your layering is correct). Give it a shot if you can.