I finally figured it out. The grub screw on my bondtech extruder was loose. The stepper motor would spin shaft assembly but the drive gear would only turn sporadically. I put some locktite on the grubscrew, put it all back together and its working great and the E steps are the same as before! For future reference if you see the large gear spinning on the shaft assembly and are getting inconsistent sporadic extrusion check to see if a screw is loose.
