Saw your post (I'm having the same trouble with an Electroliner stuck in forward) and their "Operation and Maintenance North Shore Lines Electroliners 3 Rail Version" manual says this exactly:
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Resetting Your Locomotive:
1. Turn the power off and wait 20 sec.
2. Slide the PRG/RUN switch forward to PRG under the diner.
3. Turn the power on.
4. On the CAB-1 Press [ENG] [1] [SET] (Horn blows)
5. Press [ENG] [1] [AUX] [8] (Hold for 3 sec, Horn blows)
6. Turn power off and wait 20 seconds
7. Slide the PRG/RUN switch under the diner to RUN
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I also received this in an email from Scott Mann yesterday which is pretty much the same thing assuming you know the other detail about power off and on and such:
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If you have TMCC, try resetting the Radio Board.
Program Switch to Program
<ENG> <1> <Set Button>
<ENG> <1> <AUX1> <8>
Power off, then switch to RUN
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Also, I will send scans of their manual to your email address.