Products all have 1 master_categories_id and this is the one used for pricing for things like Sale Maker ...
You can Link the Product to as many Categories as you like, but you have to decide which Category "owns" that Product ... this is the master_categories_id and this is where Sales from Sale Maker will built the Product display price based on that master_categories_id ...
So, if you need all the Products in categories_id 23 on Sale, then you want all of those Products to have the master_categories_id of 23 ...
If you go to the Product and hit C for Copy ... at the bottom is the Multiple Categories Links Manager ...
There are settings in there to update all the Products in a Category to a new master_categories_id ...