You're probably ok with your practice. Some specs mention that you can lap or hone a peened surface as long as you can still see the bottoms of the dimples (dents).
In fact, some reports show that surface honing actually increases fatigue life since it removes the minor surface damage caused by the surface dents while leaving the sub-surface compressive stresses. Just be careful that you don't do abusive grinding or allow the surface to get hot enough to relieve the compressive stresses.
