Why are my attributes for faceting being deleted when reindexing in Shopify?

If you configure facets in the Algolia dashboard they will be overridden by reindexing operations from the Algolia Shopify app. This will reset or remove any changes that were made in the Algolia Dashboard.

Solution: 

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.