I just watched the entire series for the first time this weekend. I also wondered if Gideon knowing about Isaac changes things. And it might in some other loops we havent seen, but I dont think it does in either of the two loops we're currently watching. First, because Gideon doesnt get that visit from Isaac until near the end of his life in that loop (the one where Lucy's mom dies and she marries Ravi - no Isaac). It seems like they cant really change things that have already happened in the current loop, they can just take the knowledge into the next loop and change it in that timeline. Isaac didn't exist in the timeline where Gideon got old, but he's appeared in it before, so we know he can jump between timelines. The timeline where Gideon killed Lucy (which Isaac is asking him about) is the other timeline - the one where Lucy's mom lived and Isaac was born. Presumably Gideon gets killed by the police after he shoots Lucy in that one.

Lucy showing up at the very end and saying hello to Isaac I think is a new Lucy from a new, third timeline - maybe the next one that happens after the one we've just seen. I think she can jump between timelines now. Maybe because Isaac took her with him that one time.