Not sure if I'm being dumb (spoilers)

[Thomas]

The only way to fix this is to reload from an older save earlier in the same map. (should be one after you exit the shuttle)

So you need to play through a bit, but shouldn't be too hard when you know the solution.

Very sorry about this.

The beta patch has fix for this (but you still need to reload patch):
https://www.frictionalgames.com/forum/thread-30855.html