Yep, many times unfortunately.
However, it only occurs when the new universe is screwed up.
Had Walter and his bodyguards trying to extort 100K for the artefacts at the Lodge, then Andreaj trying to kill me at the Lodge, then Sam’s daughter waiting for me for revenge for letting Sam die, then six different versions of me at the Lodge!
Each time I was unable to save or access the inventory so had to reload prior to the Unity and when it finally worked properly again it was the regular Constellation crew at the Lodge instead. Talk to Sarah, etc.
I’m beginning to wonder if it’s on purpose by Bethesda, maybe they just want to show you a messed up universe rather than us actually try to play the game within it.
I’ve being trying to whizz through all the NG+ so that I can finish the game off properly at NG+10 but it is starting to become a bit of a drag. Up to NG+ 5 I think but I’ve lost track.