If you've told your shipyard to upgrade a settlement/oil rig/mine then it just loads the cargo ready for upgrade
To actually do the upgrade you have to bring up the world map, and somehow find the right node amongst a heap over very similar icons.
Please add a button to the shipyard which instructs your ship to just deliver the cargo and upgrade from there
Add button to deliver cargo, from shipyard (for upgrades)
Quality of life
World Map & Ships
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