Hi Joe,
By now you may have found a solution to your problem, but I think, it might be useful for others, what I would like to share here.
I built a magnetic loop antenna using one of those large vacuum capacitors tuned with a stepper motor. I ran into the same problem as you, how does the system "know", where the stepper motor was left off the last time before power was turned off.
I decided to solve this by saving the current stepper position in the EEPROM, as I tell the Arduino to go through the shut-down process. Well, so much so good, but what if it is turned off by pulling the plug. I found a solution to this as follows:
I use a buck converter to power the Arduino. On its input, I have 19.5V, which is also powering the stepper driver, but on its output, I obtain 9V for the Arduino. I put a small circuit between the buck converter's output and the micro-controller: a 10 Ohm/2W resistor and a rectifier diode shunted with a 50,000uF capacitor. The resistor is needed to protect the buck converter from the large inrush current. The diode is making sure that current is not going to flow back to the buck converter when it is off. The capacitor holds the voltage for long enough (1-2 secs) for the Arduino to save the current stepper motor position.
One more thing, the Arduino is monitoring the voltage at the input of the buck converter, and whenever it drops from 19.5V to 15V it triggers an orderly shut down, saving among others the position of the stepper motor.
On start up, the first thing it does is, it reads the EEPROM to find the stepper motor's last position. Of course, I assume that there is no loss of steps over time and calibration is only needed very infrequently. I am not using a closed loop system with an encoder to have positional feedback.
I hope it helps someone. Wish you all happy home-brewing.
Best regards and 73,
Steve, n9eu