Here is my problem.
Internally Peening of a 2014-T61 Aluminum aircraft Part.
Part is threaded internally with a 6" I.D. modified buttress thread and peened after threading to .007A2 - .009A2 using S-110 Shot.
Then the tops of the threads are machined off (Truncated) creating a flat which is approximately .075" wide.
The problem is that the truncating operation leaves a very small burr that creates an interference with the mating nut.

Found that using a 3M Radial Bristle Disc 3" x 220 grit or Weiler 4" x .022/320 grit NFA Brush removes the burr and in doing so does remove a very minor amount of material on the peened threads. Under10X, Peened dimples are still very visible .
I have not taken any dimensional measurements, but feel that I have not removed more than 10% of the intensity.
My question is will lightly polishing a peened surface alter the positive effects of peening?

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.