Does the a4988 have any sort of back emf protection? If I manually rotate the stepper motor 20 revolutions or so while its connected to the driver (while its not powered) will I run a high risk of ruining it or the arduino connected to it?
A4988 is a deluxe driver, so I think it has internal protection circuit for EMF.
Look at the Functional Block Diagram (in page 3) :
There is protection diodes connected to FETS
You should be careful about what you are expecting of this back EMF protection. Any MOSFET-based H-bridge will automatically have diodes across the MOSFETs to limit fast voltage spikes from the inductance of the motor. However, if you just spin the motor, it will act as a generator and that voltage will basically go through to your power supply. To see how this could be a problem, imagine that you have a circuit that can operate up to 16V that you normally run with a 12V battery and your motor runs at 100RPM at 12V; if you manually spin the motor at 200RPM, it will generate over 20V, which could destroy your electronics. The voltage/speed dependence is easiest to understand with a DC brushed motor; it’s more complicated with a stepper motor, but the voltage you generate still goes up with how fast you spin the motor.