You are able to control which supplier part number is shown in the BOM using the preferred checkbox in the supplier part number tab.
The BOM view still displays the internal "genuine" part number as well as the "preferred" supplier part number as well.
Does this give you what you need ?
It does and doesnt fix my problem.
This works on a system wide level, but if on two drawings we want different suppliers then this would mean continusly changing the preffered supplier for all parts, which isnt possible.
Ideally we would also like the 2nd version of the part (which has a different part number) to be searchable in Vesys components.
I feel like it could be done with the alternate part box, but I cant figure out how to use this in Vesys design/harness.