[SPOILERS] Are the chioces even tracked by the game at all?

[RawkBandMan]

Spoilers, of course.

If you choose to delete any of the legacy scans, the game remembers this when you later have the opportunity to use those or a dummy for the simulation, so some stuff is tracked.

The game also records whether or not you kill WAU, because you'll be missing a hand, and the dialogue with Catherine is different (she asks about the missing hand).

Apart from that, I noticed no gameplay difference.

There's also some minor dialogue differences when going in the climber that change depending on if

Spoiler below!

you killed Simon-2 or not