You need to work with item requirements from the project, so that the project is linked to the manufacturing order, not sure if you can link it manually when the manufacturing order is created.
However, it is not possible to inherent the project id to the "sub" manufacturing order. So if you have an Item A consisting of items B & C, which are both being manufactured, you can create an Item requirement for item A, but it will not be inherent to B & C, so if B & C is batch controlled, you arent able to link it to the project.
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