I have an Assembly item that when I build it, I relieve inventory the components and increase the finished good, as you would expect. However, I also need to remove a part from one of the components (which would then add inventory to a different part to sell it individually).  Basically a Work order that relieves inventory of components, adds inventory of its finished good, and then adds inventory of another part. Is there a way to do that in a single transaction? I tried playing with negative BOMs, but I could not save the item.

I dont think this can be done with a single transaction. Likely you will need a second work order that increases the inventory of the other part (assuming it is an assembly)