If the decoder LED output is current controlled, you could put the resistor in parallel with the LED, to divert the unwanted current from it. Try 1k and see what happens (in parallel, a higher value resistor will increase the LED brightness).
The ditch lights are on F1 and F2. They both connect to the blue common. Not sure how the Digitrax DN613K1C drives the flashing lights. I'll try the parallel resistor to see if that changes anything.
FYI, it's DN163K1C , not DN613K1C. I assumed it was a typo the first time, but since you have 613 again, thought I would make sure you know what it is. I am fairly certain the DN163K1C outputs are not current controlled. If you do try the parallel resistor, make sure you still have one in series with the LED, otherwise it will likely blow. I don't kow if you saw before, but I was wondering if you have a manufacturer and part number for the LEDs. I'm really curious what the specifications are.
LEDs were from Ebay. Not sure of the details. Tried it in parallel with both 1k and 3k resistors. Didn't light with the 1k and did with the 3k but no noticeable difference.