The following queries have been removed from Headless Server Schema:

commerce/productAugmentationBySite
commerce/productAugmentationByStore
commerce/categoryAugmentationBySite
commerce/categoryAugmentationByStore
commerce/augmentationForCommerceIdBySite

Use the available queries below content root instead:

content/categoryAugmentationBySite
content/categoryAugmentationBySegment
content/productAugmentationBySite
content/productAugmentationBySegment

(CMS-23704)