You can reset the Viper200 and not need to home the axis. It just clears the internal counters and holds where it is.
You would need to only power the encoder +5v from the EMC board and not connect the +5 encoder power from the Viper.
Grounds between the EMC BOB and Viper control side would need to be short and well though out, so encoder signals don't get corrupted.
I think EMC outputs step/direction, doesn't it ?
Larry K
Manufacturer of CNC routers and Viper Servo Drives
www.LarkenCNC.com and www.Viperservo.com