I remember seeing a post about this a while back but couldn't find it. On a Legacy H-16 the lights blink 3 times and repeat. I did a reset and it was fine but after a few minutes it started up again. Also the smoke unit stopped working (no motor sound). All other functions work even with the lights blinking.
Thanks for any help.
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From the manual...
It will most likely have to go back to Lionel CS.
1 Main drive motor stalled.
2 Smoke 1 element problem.
3 Smoke 1 fan problem.
4 Not applicable.
5 Not applicable.
Marty is right. You have a defective smoke fan motor.
Thanks guys
It could simply be that you over-filled the smoke unit and it has drowned the motor/electronics. Sometimes this will recover if you leave the smoke switched off for several days (About a week at most.). If you can spare the time, it may be worth waiting before you ship it off for a repair. 
Nicole's idea is certainly worth a try. I've had one that was blinking 3 and eventually subsided. But then again I got a smoke unit resistor indication a few weeks later that wouldn't go away.
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