Prevent categories from being overwritten during a Product Set update
By default, the Product Sets plugin will overwrite any category customizations you have made to a product when the Product Set updates. Generally, ALL product-category associations should be made at the Product Set level.
If however you need more control over the categories your products appear in, you can use the following code to prevent your custom product categorizations from being overwritten during a Product Set update.
Create a custom plugin
If you haven't done so already, create a custom plugin.
Add the following code to your custom plugin:
Save your custom code.
This code will prevent any product category customizations you have made from being overwritten during a Product Set update.