This sounds like there's more going on than you thought. Do you have any payware content offline? That can cause that huge number of missing dependencies, which cause a fault-reporting. I deliberately setup a filter to show missing dependencies only. That solves that confusion so I know it's only missing stuff and not other errors as well.
When weird stuff like this happens, I highly recommend trying an EDR. Press CTRL while clicking on Repair database.
When merging, never merge sessions. Weird things can happen. Merge Routes always. When merging sessions, consists lose their position and can end up at 0,0 world-coordinates, or somewhere like out at sea. I did that once and ended up starting the merge over because there were consists out in corn fields, off in space, and gawd knows where else.
I have had, and reported too, the floating or buried assets. To repair that, I got the ground height and applied it. This caused the assets to level out to where they should be. If I made a bump or divot, hitting undo fixed that. It's a pain because you can only do a small area at a time, but it's good workaround, but N3V is looking into it.