Well this is a bit of an oddity. Had reached the part where i was in the belly of the beast with the probe gun. Got fed up after almost finishing it and having to do the whole thing over again. Saved and left.
When i returned well..
I started quite a bit back (at the area around the junction to the armory and the other warehouse) had to retread the entire trip back. Found i had to build the probe gun again. And also that i had to equip the new probe gun since the old one would not trigger the necessary response.
All in all. Quite confusing.