Did you do it your self or by a shop? Even if you did it yourself the shop needs to use the Specialized Studio software to sync everything. As far as not starting, the main battery connector may not be seated correctly but the shop should see that when it's connected to the program.
Motor replacement was done at certified Specialized shop. But how do you explain that when the RE was connected the bike functioned fine?
Take it back to the shop. They probably did not correctly install the main battery connector. I assume when you look at the TCU it does not show either the blue bars (original version TCU) or 150% if you have the MasterMind version TCU. The system is designed to work with just a RE. The RE and main battery are wired in parallel so you can have one or the other or both. This is so you can fly with the bike by removing the main battery and carry on one or two RE's. Seems like they should have noticed when the hooked up to the software.
