Do the drives have a Home and Index sync option.? Some drives will let you connect a switch to Home input on the drive and then they will sync the index pulse(z) of the encoder to position the motor.

What controller are you using.? Some controllers like the Cslabs will Home to index pulse or a set number of pulses after home switch detection.

Regards E-stop then you should always assume position is lost after hitting so therefore need to re-home to ensure accurecy. Like Eddy says E-Stop is emergency so should Kill power. Feed hold or pause or general stop is a controlled halt and doesn't lose or require homing.
Like wise a Limit trip isn't really an emergency situation it's a positional error so I wouldn't kill power to this action just halt drive outputs and inform controller it's happened. This will keep the drives powered and holding torque but really you will still have lost position thru inertia etc so homing will be needed.