Paintless dent removal will not cause any long term side effects to your paint. The only effects to the paint would be if whatever caused the original dent caused damage to the paint.
Paintless dent repair relies on metal memory and the ability of metal to hold a position. Metal panels can usually take a certain amount of deformity and will reform without any visible damage. When you get past the point of elastic deformation, you get into plastic deformation, where the part will not rebound. The paintless dent repair person reverses the effect of this by pushing the dent from the backside and pressing it past the point where the panel is flat, so it will once again form back (rebound back) somewhat to where it should be in the first place. Most of the guys I've seen do this make it look so easy, yet come out with awesome results. First time I saw it in action I was truly amazed. They'll usually go through existing holes in the door or panel to make this happen. Sometimes drilling is required, but it will be in a not so obvious place.
Again, as far as the surface of your paint goes, there shouldn't be any worry about chipping or flaking if the process was done right. It should look good as new. At least that has been my experience with the guys who come to the car lots to fix the minor dings.