Abandoned ship systems disappeared?

[Kazeto]

That's generally not a problem if you have the scanner away team item, for as long as you remember to get back to your shuttle after cleaning a level on which you'd found a large item.

Well, generally; sometimes the level is divided in two and you just can't get to the other part, in which case there might or might not have been an item but it's not like it really matters since you wouldn't get it anyway.