So there is no way that I can find to get to the interface to upgrade your pirates or change their outfits while the fort is upgrading, which is probably intended - you can't train any other troops while AC/VH are upgrading. Unsure how you'd be able to switch between Legendaries during construction either, as that seems to be in the same interface, but thats mostly unrelated. However, if someone attacks your island, you can still go to the fort when you're checking legendary stamina (presumably as a way to switch to a different legendary or put him into rest mode). And as soon as you get here, you can now change your outfits or start training (assuming you have the required materials). So either we're intended to be able to get to that screen during upgrading, and I'm just dumb and can't figure out how - or we're not supposed to, but getting attacked lets us in there anyways. Either way, I'm currently upgrading the fort and upgrading boomer at the same time, and the quirks around how I was able to do that made me think it was unintentional.
Was just about to post this formally. It has been acknowledged as a bug by Midoki staff, both the Legendary Fort and Trade Ship icons should still be available during an upgrade. As outlined, you can access the Legendary Fort after being attacked as a workaround. In addition, you can access the Trade Ship using the icon at the top right (well closer to top centre with all the clutter there now) during an upgrade.
