Hey Boaters Planet - I'll take a stab at this if you haven't figured it out yet.
I do know that if you upload a product with a Model# that already exists, but the category is different, that new category will only be linked product and not a NEW master category. So what you do to change an entire category of link products to a master category is navigate in your ADMIN/Catalog to your list of products. Then on any of the products click the C for copy at left. Once the next page at the bottom left you'll see a button called "Multiple Category Links Manager". After clicking that you see a list of ALL the categories you have created. if the product you are looking at is in more than one category then more than one category will be checked. the one that is yellow is the master category. So if you see that you want to change that product;s master category AND all the products in that category along with it, look at the very bottom of the page where you'll see "Reset ALL Products in the selected Category to use the selected Category as the new Master Categories ID ..." enter the number of the category you want to be the new Master category and viola! It changes.
I hope this helps! I'm sure why the category you created disappeared. Hopefully there's a logic explanation for that.
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