By default, the attributesForFaceting configuration (facets) is handled by our plugin for Shopify. If you edit these configurations directly on your Algolia Dashboard, they will be overridden when you run a reindexing operation.
You can find more information about this in the following article: Which settings are handled by our Shopify App?
There are two options for preventing overrides.
Option 1 (recommended): Configuring facets directly on the Shopify App
When configuring facets, all changes should be made in the "Facets" configuration section of the Algolia Shopify app, (not the Algolia Dashboard).
In the Algolia Shopify app go to:
Search Options > InstantSearch > Customize > Facets
This will show all of the default facets, along with any custom facets that have been added via Named Tags or Metafields. To add these facets you need to click on the + icon and save the configuration.
Option 2: Disabling the default synchronization functionality for your facets
Finally, if you wanted to maintain your facet settings when configuring your facets in the Algolia dashboard instead of on Shopify, there is an option to prevent the default synchronisation functionality: