I find a gap in the portal 2 timeframe!
There is a point where GLaDOS says:
"This test chamber was designed by an enginner that has won a nobel prize, I don't know for what though. I do know it wasn't for being immume to neurotoxin."
This is one of the modern test chambers (al be it overgrown).
There is also a dialogue that was never added where Cave puts Caroline in GLaDOS, and as the final line in that she says "I am awake. And I am going to kill you all".
Wich means that everyone died when Cave did. Cave lived in the 1960-70s with the retro chambers. So how can an engineer have designed a modern test chamber when he died in the 70's?
Just because she says, I'm GOING to kill you all, doesn't mean she did.
How do you know for a fact that all the chambers were still retro?
How did you know that she killed them right away?
How did you that GLaDOS didn't rebuild the test chamber if it WAS retro?
How do you know that everyone was killed along with Cave?