When using the Algolia Shopify app, the facets should not be configured directly in the Algolia dashboard Facets section. This may work temporarily, but when any settings changes or reindexing are performed, the configured Facets may be overwritten.
Instead, all changes should be made in the "Facets" configuration section of the Algolia Shopify app, under 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.