Sorry for late answer… Consolidate script makes new image consisting of all different textures of object. Initially these are each mapped on separate UV layers. In order to use consolidated image as texture it needs to be used on default UV. Since it combines all texture parts they are not needed anymore.
What i did is took some 3 images and applied to some sides of default cube, each on separate UV, run Consolidate script and get one big image consisting of all 3. Saved that. I deleted all textures from cube and made new one, setting consolidated image on default UV. That gave same result as applying 3 different images on 3 UVs.
Happy blending!