So, in the first blue universe, William Bell is head of Massive Dynamic. He did all kinds of experiments with Walter when they were younger, Walter ends up in St Clares, Bell goes on to head up Massive Dynamic. Eventually, they get back together to help Olivia cross over to the red universe. In the process of going to the red universe and back, Bell dies.

In the original Red universe, Bell never formed Massive Dynamic. If memory serves, he died in a car crash. I'm not sure about that, but whatever it was, he's not around, and hasn't been for a long time.

So in this new Amber universe, Oliva never discovered her powers, and never crossed over to the red universe. So, logic follows that William Bell should still be alive. Except he isn't. His history is practically the same (he still did experiements with Walter, gave Oliva cortexephan, set up Massive Dynamic etc), but he's not there. Walter talks about him in the past tense, and Nina is head of Massive Dynamic (it seems like Bell either never gave the ownership over to Walter, or his will was not discovered). So what happened to him?

TL;DR I can't work out how Peter getting removed from the timeline has caused William Bell to still be dead, even though the events of his death can now never have happened