This has been going on since a recent update: the GP38 in YN2 livery has completely disappeared- or, at least, its slot in the selection screen still exists, but it has been entirely replaced by the YN3b version (which isn't just a different paint job; the physical model is different). Possibly related is the fact that custom liveries for freight cars no longer spawn at all- there is nothing now but game-default CSX in the yard. Even weirder, one DOES get ample Union Pacific locos subbed in.
