Should the player end up with two PRTs in a game, only one of them gets marked / tracked on the map even after both have been discovered. I'm not quite sure which of the two, but I think it's whichever was discovered second.
In between (re)loading saves of a game with two PRTs, I think there also was one time when I "rediscovered" one of them, as in, I got the "PRT discovered and added to map" message again, however, I think it was not even actually added.
The logic that tracks the discovery state and map marker of the PRT(s) appears to get a bit confused when there are two of them in a game.
(There also was an odd occurence where the "Inspect PRT" interaction hotspot for one fo the two PRTs parked close to one another could be accessed even from about 10-15 meters distance, while the other was working as it should, but it did not persist through a save and I couldn't recreate it so I have no idea what could have caused it.)
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