What do you mean by "save the game? Run a session and close before the end, saving the progress? Or close surveyor saving the entire route?
If you're running a session, then it's all under the quirks of the game engine that "forgets" any previous setting such as industry loads and waypoints when you exit and save, it's a well known issue (and a difficult one to work out apparently, for the developers).
If instead you're working in surveyor and on the session layer (by accident or on purpose doesn't matter), you need to save both route and session, and when you restart work you MUST open the session - not the route alone - for editing, or you won't see the previous work done in the session layer.
Not everyone is aware of the fact that opening the session for editing opens the route too, it's just a matter to select a route layer and you can work on the route itself (plus you can add anything in a session layer, not just trains); BUT, if you never select any route layer, all your work is saved in the session only and you will have a hard time finding your edits if you edit the route alone afterward.
I usually lock the session layer when editing a route, that way I'm sure nothing goes where it's not intended to go.
In brief:
1) need route editing? edit the route and avoid the session layers at all costs
2) need to build a session? create/edit a session and avoid the route layers at all costs
That said, Viraf, check the route sessions and verify if you haven't saved your work into one of them by accident.
Also be sure you cloned the route if you happened to work on a DLC route (I'm not sure if that's the case for freeware routes too) and you're working on the cloned instance, I hit that wall myself and I know how hard it is LOL.
When you clone a route, infact, the game doesn't switch to the new saved instace like almost all other software does, but it mantains the original instance in memory and you keep working on something you can't save after, unless you use the "save as..." command every time ending up with lots of routes with the same name but different edits in them (I guess they have different KUIDS too).
Breaking down the steps:
1) clone the route
2) close surveyor
3) open the CLONED instance
4) enjoy!
Sorry for the wall of text, but it's not easy to pin down the issue without being in front of your monitor while you play.
Luca