Resting was designed for sites that do not have master_categories_id as they import their products and do not use the Admin ...

If you already have master_categories_id in your products table ... then you do not need to reset them as they are already there ...

What you should do is determin, based on your Category structure, what Category "owns" the product so that you can set the Master Category ...

If you walk down aisle A in the store and find a widget on sale for $10 off ... then walk down aisle F in the store and find the widget ... it should also be on sale for $10 off ...

Just because it is not in its "main" aisle does not change its price ...

You need to determin what Category owns your products so when you put a category on sale ... the product goes on sale everywhere regardless of the Linked Categories that it may be in ...

NOTE: You can also use the updater on the bottom of the Multiple Categories Link Manager to set a given Category as the Master Category for all Products that are in that Category ...