Thst's what happen when I open scenario in RWTools Editor to swap rolling stock:
Missing items:-
C:\Program Files (x86)\Steam\steamapps\common\RailWorks\Assets\RSC\P42Pack01\archive\RailVehicles\Passenger\Amtrak_phIII\Baggage\SL Baggage_phIII.bin
C:\Program Files (x86)\Steam\steamapps\common\RailWorks\Assets\RSC\P42Pack01\archive\RailVehicles\Passenger\Amtrak_phIII\Coach\SL Coach_phIII.bin
C:\Program Files (x86)\Steam\steamapps\common\RailWorks\Assets\RSC\P42Pack01\archive\RailVehicles\Passenger\Amtrak_phIII\Coach\SL Coach_phIII.bin
C:\Program Files (x86)\Steam\steamapps\common\RailWorks\Assets\RSC\P42Pack01\archive\RailVehicles\Passenger\Amtrak_phIII\Sleeping\SL Sleeper_phIII.bin
C:\Program Files (x86)\Steam\steamapps\common\RailWorks\Assets\RSC\P42Pack01\archive\RailVehicles\Passenger\Amtrak_phIII\BaggageHeritage\BaggageHeritage_phIII.bin
C:\Program Files (x86)\Steam\steamapps\common\RailWorks\Assets\RSC\P42Pack01\archive\RailVehicles\Diesel\P42DC\Amtrak 40th\Locomotive\GX_P42_Amtk40th_nc.bin
C:\Program Files (x86)\Steam\steamapps\common\RailWorks\Assets\RSC\P42Pack01\archive\RailVehicles\Diesel\P42DC\Amtrak 40th\Locomotive\GX_P42_Amtk40th.bin
I have no idea why it references to P42Pack01\archive\ folder
I have "normal" P42 unpacked from .ap archive, so it has full content unpacked.
and \archive is my backup folder where I keep original .ap
Scenario normally runs in the game, without any missing stock items.