No, the master rep cannot be replaced with the quick rep. If you fix the components in the quick rep, they should regenerate in the master rep. The components may have regenerated in the quick rep because mating components were missing. If components are missing references in a simplified rep, a missref.lst or something like that is generated by Pro/E. The only true way of getting the components to regenerate properly is by being in the master. An easier way of working with the master rep is to have all components on layers and blanking layers you do not need.