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I am dealing with a very complicated product system. The system consists of many interlinked processes along the production chain, resulting in one final product, let's say product A.

I need to create product systems for product B, C and D having about 90% identical production chains, similar to the production chain of product A.

Is there a way of copying the product system and changing the final production steps? For all I understand, it is not possible to change the reference process after a product system is created (in this case copied).

Using the auto-link option is not possible, as I know it will make many incorrect linking assumptions.
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In a product system that produces now B, you can try to add the new process that produces C e.g., then change the product system reference to this new process, remove the links (not the supply chain) of the process B in the product system, then add the links to process C, and then remove process B (assuming process B is not used elsewhere in the product system).

Edit since you bullied my colleague over his cell phone to get an answer immediately or utmost today since you are needing this in a paid project:

Try this sql code for the change of the reference process; I did not test it on your case but it should work. I am assuming the unit of the two products is the same, the amount is the same, the new process is a production process, and the new reference flow has only one flow property. You can only calculate if the connections are closed again, i.e. connected. Replace the # with the UUIDs of the respective elements.

update tbl_product_systems set f_reference_process = (select id from tbl_processes where ref_id = '#'), f_reference_exchange = (select id from tbl_exchanges where f_owner = (select id from tbl_processes where ref_id = '#') and f_flow = (select id from tbl_flows where ref_id = '#') and is_input = 0), f_target_flow_property_factor = (select id from tbl_flow_property_factors where f_flow =  (select id from tbl_flows where ref_id = '#')) where id = (select id from tbl_product_systems where ref_id = '#')

We like to provide a free software, but some people really misuse this, and seem expect that we are just used to work for free, and are always available immediately. If these are working in publicly funded research organisations that evidently have a brilliant sustainability manifesto that claims to care for human beings, and that anyhow get their salary from taxpayer money, the better. Sorry for the rant.

How do I change the product system reference to this new process? In the product system, tab "General information", I see the subsection "Reference" with the old process to produce product A.

However, now I would like to change the reference process to the process producing product B. It seems to be impossible to change the reference process.