As of GraphQL Admin API version 2024-07, you can now set available and on hand quantities for inventory via the new inventorySetQuantities graphql mutation. At the same time, the inventorySetOnHandQuantities mutation will be deprecated.
This is a companion discussion topic for the original entry at https://shopify.dev/changelog/new-set-quantities-graphql-endpoint-for-setting-available-and-on-hand-inventory-quantites