Convinced that the fault is entirely mine, but I'd like to find out what I did wrong to avoid repeating it:
Created an 8x4 train station lot, heavily borrowing on other folk's props. All went as planned and I switched to SC4T to transit enable: straight forward, two sets of rails, immer geradeaus. Saved and plopped and lo and behold, all works fine in-game, even when I had to copy & past the Query UI ID from another train station.
Then I wante to change something and from here on things went amiss. SC4T says "Error reading file"; Reader opens and saves the file without problems; LE does not even list the lot anymore, but LeProp opens and saves it without a hitch.
Edit: So, where did I go wrong? Ok, so I figured it out: I had changed the Exemplar Type to Building from Lot Configurations! Stupid move, I admit.. >:(