Bob will explain this more elegantly than I can, but:
For the moment, ignore things like friction, wind, rolling resistance, air resistance, etc.
Forget about the windings. It's a question of energy. When the system (you and the Segway) are moving, the system has kinetic energy. To slow down, that energy has to go somewhere.
If you used conventional brakes, the energy would go into heat.
If you brake using a motor, and don't have a big resistor to heat up (or a space heater or whatever), then that energy goes into (charging) the batteries.
Similarly, if you are at the top of a hill, you have "potential energy". Getting you down the hill requires putting that energy into the batteries (converting it to stored energy). Getting you up the next hill reverses that process.
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