Hello @timalot,
IO_E2 corresponds to AVR pin PE2 on the A-Star 32U4. You can find this information on the README of the pololu/fastgpio-arduino library under the “Specifying a pin” section. A copy of this library is included in the pololu/a-star-32u4-arduino-library. I believe this AVR pin is not exposed on an arduino 32U4 (micro/Leonardo) hence it doesn’t have an Arduino “digital pin” number.
Note that the Pololu boards for the Zumo, Romi and Balboa use XOR (exclusive OR) gates which combine the encoders pins A and B to use only one interrupt per side. I you plan on using the A-Star micro controller, you will either have to use XOR gates or use two interrupts for each side (pins A & B). See this forum thread for more details.
I made my own encoder library for my Romi based robot which uses the A-Star 32U4 Robot Controller with Raspberry Pi Bridge. You can find the latest encoder class files in the src folder of my DrGFreeman/RasPiBot202V2 repository. It should work fine as-is for your project if you can free pins 0, 7, 8 and 16 for the encoders. Feel free to try it and ask questions if you have any.
Hope this helps and good luck with your project!