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Illanair

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Transport ships aren't visible on the design screen, and the game doesn't upgrade things like engines to provide longer travel distances, which is a wee bit of a problem when your armies can't physically reach enemy systems.
 
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jakt

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This is actually game breaking in non-elliptical galaxies if you are unable to have a foothold to build troops with on the other arms of the galaxy.
 
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Palleon

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Have the same issue myself, my transports are unable to leave my "arm' of the galaxy, so I can't really do anything as they can't go where all my other ships go. They all have Warp Drive 1 while all my other ships are at 2.
 

Maeglys

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There is a workaround currently.

If you "check" the box to enable the Auto-complete design, it will update the transport ship to the latest design. It will also however create a bunch of design you might not want.

You can safely uncheck it after and delete the extra design. The transport will stay updated with the best tech that was available at the moment you check the box. If you ever need to update them again, re-check the box.

The bug is probably because you should be allowed to design the transport ship class in the ship designer, but you currently can't see it. AI empire will probably won't suffer from this bug since they probably use the auto-update feature by default.
 
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jakt

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If you don't care about achievements I made a mod that allows you to upgrade transports in the fleet designer http://steamcommunity.com/sharedfiles/filedetails/?id=682701139

As noted, an alternative that works to downloading that is to set in the bottom right of the fleet designer to "Auto-generate designs", then unclick it. If your transports are not loaded (boots on the ground), IIRC, they are auto updated without need to press upgrade fleet button.