In my current game, started on 1.82, I had a trade route established with the home world of a custom race, The Gratification Corp. This was a very long established trade route.
They then defined a UP vote. After that, the Diplomacy window showed that they were no longer trading with me. My Govern window Trade tab shows that I now have an additional trade route available, and that the trade route that I had established with their home world, along with two other trade routes they had established with me, are are no longer listed.
Ok, fine, so defying the UP vote did away with all of their trade routes. I have to assume that's working as designed.
But now I send a freighter to their home world to re-establish a trade route, and when it arrives I get the pop-up message that tells me that the freighter can't create a trade route because I already have a trade route between these two planets.
So there's definitely a bug here. Either (1) the trade route is there and is not being shown correctly on the Diplomacy and Trade windows, (2) the trade route is not there and it should allow me to create one, or (3) Civs that have defied a UP vote aren't allowed to trade at all, in which case the pop-up message I got is wrong and the Diplomacy window that shows them trading with another civ is wrong.
Edit: Forgot to mention that the trade route does still appear on the main map.