Had to conduct some investigation myself. Apparently, MJ devs has moved Ascent Guidance from 90 level node it was in 1.8 to 300 level node it is in 1.9 but since my original savegame was from 1.8 it kind of "retained" already discovered part of tech tree on transition. Except that retention did not work for MJ tech, only for native tech. This is why I now see Ascent Guidance module in both 300 and 90 level nodes at the same time but it does not actually appear.
That's crazy but at least holds some logic.