Master Categories ID and linked products

I am having an issue with getting Update ALL Products Price Sorter to process without crashing. I previously had products linked and I deleted these linked products without paying attention to whether I was deleting Master id or not. Then I noticed this warning when trying to delete a category via test site

Linked Products whose Master Categories ID are deleted will not price
properly. You should first assure that when deleting a Category that
contains Linked Products that you reset the Product(s) Master Categories ID
to another Category before removing a Category

I think this is why I might be having issues with Update ALL Products Price Sorter. I am wondering if their is a work around. I am able to Reset ALL Products Master Categories ID but that doesn't seem to do the trick.