Just in case anyone else runs into this particular situation, I went ahead and scrapped all the private sector's ships and they rebuilt them to the Mk2 designs. I'm not sure if there's a more elegant way to solve that particular problem, but it worked well enough for me!

<t> Sorry if this should be posted in the tech forum, but I'm not sure if it's a bug or if I'm not understanding a mechanic.<br/>
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When designing my initial Freighters, I changed the Default Retrofit Stance to Manual Order. Upon researching warpdrive precursors, I updated the design and with ...