From Railsimulator Wiki, Railworks Documentation, Reference Manual, I found this only 2 weeks ago

it's awesome!!!
Wiki wrote:Q: Can I preset the direction junctions for my scenario?
A: Yes*. It is possible to set the state of a manual junction in a route via the Scenario Editor. Simple open the 2D Map and operate the junction by Shft+Left Clicking on its node to change its direction. These changes will then be recorded when the scenario is saved (This information is held in a file called InitialSave?.xml).
This allows you to pre-determine a route through a yard for the player, or if your route features only manual junctions, a path for the entire scenario.
•Please note, that this function does not apply to Automatic Junctions (junctions with no blue node shown in the 2D Map, and no lever next to the track). These junctions are controlled by the signalman at all times.
About your question, the player can always change manual junctions, despite of its initial state. Only automatic junctions are locked by AI traffic feature, player can not change the state of automatic junctions, never.
And finally, be sure that no AI Train will pass over (and change) the same junction you have preset for the Player train.
Cheers,
Doc.
Who doesn't have dog, hunts with cat.