You can't just keep a count and hope they will remain in step, you need to calibrate it every time the power is applied.
Remember you have a limit on the number of times you can write to an EEPROM location, it might be 100,000 times but if you are writing at the rate you are sending steps it will fail soon.
You need to reconsider what it is you are doing, you don't do stepping motors like you are suggesting, you need some form of feedback or absolute position indicator.