Stock has one owner: Commerce

Stock quantities now live in Commerce only. The Catalog shows them read only, on the product page and in the variants table, with a link to Commerce › Inventory where they change, and the Inventory entry is gone from the Catalog menu.

Imports, the Catalog API and Atomo set stock only as the initial quantity of a new variant. Afterwards a stock line is skipped with a note (imports) or refused with a clear message (Catalog API), so the numbers you see everywhere are the ones Commerce reads from Shopify, or writes there when Nucleo runs your orders.