I was getting this same error because the key parameter on my checkout id was changing faster than I was keeping it up to date in state. You could try making sure that the key is accurate and the latest version.
Topic summary
Issue: checkoutAttributesUpdateV2 returns “checkout not found” when attempting to update custom attributes on newly created checkouts via the Storefront GraphQL API.
Context: A webhook (checkout/create) triggers the mutation with a checkout ID like gid://shopify/Checkout/36603304411456 and input including allowPartialAddresses and customAttributes. Base64 encoding the ID was also attempted without success. The mutation/code snippet and variables are central to the discussion.
Guidance: Shopify support notes the mutation expects a checkout ID that includes a key parameter (format: gid://shopify/Checkout/{ID}?key={KEY}), as documented in the Storefront API guide.
Latest updates: The OP tried including the key and Base64 encoding but still encountered the error. Another user resolved a similar issue by ensuring the key was current; a stale or out-of-date key caused “checkout not found.”
Action items:
- Use the checkout ID with the latest key from the most recent Checkout object.
- Keep client state synchronized; re-fetch/update the ID before mutating.
- Avoid relying on older or encoded IDs.
Status: No confirmed resolution from the OP; discussion remains open.