We created a special work order. We then build the assembly through the Assembly Build. Now we do not want fulfill the special SO. So, we closed it. For some reason, we cannot select the build assembly lot number in other SO. Any reason why is that the case?

The linked special WO means you can only use the inventory from that WO to fulfill that SO. Your inventory is now stuck. The only way to fix is to delete assembly build and WO and recreate without the special WO link

What if the period is already closed?

You could try to an inventory adjustment. Adjust out the inventory then adjust it back in using the same qty, rate, inventory detail and lot It should be available then

We tried that but we could not adjust it out similar to the sales order.

You could un-close the line item and then fulfill the line item. Then post an adjustment to bring the item back into inventory (posting against the same customer/project and COGS account). Then the COGS of the adjustment would offset the COGS of the fulfillment. Then close the line again so it doesn't get invoiced

That makes sense. Thank you.