I am also having this issue periodically on some stores. Usually it’s with thousands of products and there can be up to 10000 missing, but I’ve had just a few products missing from a small bulk mutation.
This is quite urgent as we have no error message or anything to explain to the user why the task failed to edit all items.
https://community.shopify.dev/t/bulk-mutation-not-editing-all-products
I can provide more recent failure examples with bulk operation IDs if desired. e.g. gid://shopify/BulkOperation/6387664552188 or gid://shopify/BulkOperation/6698591355155
Also I should mention this is happening on 2025-10 for productUpdate mutations as well, so not limited to just variant editing. The second ID provided is an example of that.