Well thats very strange, I've tracked down the area in SnC in TANE and there is nothing missing from your screenshot, I don't have the orange boxes and there is nothing showing where they are, looking like the route has got corrupted in some strange way.
I'd suggest having a look in the packages folder, move any sc379 folders there are 5 of them with different suffixes and put them somewhere safe, in case this doesn't work! Run a database repair so TANE knows it's gone, close TANE then restart and it should download the route again next time you enter the main menu.