Amsterdam is treated as two different cities in the yellow and green phases and so a run from one to the other is possible.In the brown phase these merge into one city which prohibits this route.
Thanks Simon. That's what we did - but I ended up wondering if we might have been taking advantage of imprecise wording in the rules.
For the sake of the record - and for anyone interested in timing - we were four players with two of the players being new to 18xx games and we took precisely 3 hours. But that was with omitting the Private Companies altogether, which I felt would only add to the confusion fore new players and would also lengthen the game.