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I was just told in-game in DPS-Diamond of a workaround for stuck x-traits. If you aren't aware of what that is, x-traits are getting stuck with whatever was first put into them and swapping back to it on map change, such as entering a TFO.
The workaround for stuck x-trait seems to be to go to ship manager, select trait from inside manager, swap ships, swap back; if it's not fixed, try again.
The workaround for stuck x-trait with multiple x-trait ships seems to be similar: go to ship manager, select trait from inside manager, swap ships to another affected ship and swap that one's trait, swap back to the original ship; if it's not fixed, try again.
I've tested the first method thus far and it works.
Hope it helps someone having a problem with this issue.
Discovery is good, it's you that sucks.