Or you can uncheck it before saving. Tecnically, the special work order put the flag on the line of the sales order taking it from the assembly item master data. You can change it manually, removing the flag (check if maybe it’s hidden).
If it’s already created, you have to delete the WO and the you can remove the flag.
I think you can try to create a workflow: if you show the quantity available (I’d use that rather the on-hand), then deflag the special work order field in the sales order, otherwise leave it as it is (so flagged, due to the assembly item master data). Try it and see if it fits your need 😉