When you create a new assembly, how to insert a part which is already checked in from the Vault?
Just add it to the assembly like you normally would. Checked in files can still be used, they just can't be modified. Adding a part to an assembly does not change the part.
Exactly like Jim said. The parent (assembly) gets the link to the child (part) while SWPDM manages the link from child to parent for the Where-Used tab in the database. I have seen times where working on an assembly makes SolidWorks think the part was modified, but that is due to some other force than just adding it to the assembly with mates.
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