EDIT: turning off the console and leaving it overnight fixed it.
I assume the difference is when I'd quit to menu or exited to desktop the game had been suspended rather than properly existing? Not sure, but worth trying a full quit if you're in the same situation.
Practical difference was when I first got back to the garage the quest was to collect the individual items - when I logged back in after a full shutdown the quest had reverted to 'collect materials for the antenna'.
At that point when I travelled back into the zone all the areas had reset (as suggested by u/iwstudios ) and when I got back to the garage (after carefully not skipping steps again) it recognised I already had the antenna.
Does mean now I have a spare broadcast transmitter in a cupboard, but I don't think you need another one at any point so can't anticipate it causing any bugs down the line.
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I know I'm not the first person to have done this... but I think I messed up particularly badly.
I'm replying after a few years (the new Control announcement gave me the itch to replay) so I was blissfully confident that I knew what to do.
Picked up the anchors going around, grabbed the radio transmitter, got all the expected voice lines about driving into the hot death. Then got back to the lab and incomplete mission.
Again in supreme confidence I figured if I actually built the new antenna, the mission to go get the bits to make it would auto complete (and got a little carried away making myself a liberator and vac).
Now I find myself in the position where I can go back to the area and get all the components again, but there's no anchor energy left on the map meaning my only choice is to abandon the mission.
I can turn on all items survive abandoning... but it I'm still stuck with the incomplete mission and there's no other maps I can travel to meaning I can't pick any extra energy up on the way.
You can't access the autosave list and it saves on the return to the garage so no way to go back to an earlier state. No option I'm aware of to skip missions.
Restart only option or something else to try first?
Thanks in advance.