So I wanted to make something clear here:
My author's note at the end of Chapter 42 did not mean we are literally tackling Chuck vs. the Best Friend. This is my fault for not being more clear. I simply meant we were going to tackle some of the same themes--simply put, Chuck doesn't want to put his best friend in danger. Because he's Fates Chuck, he has a very pessimistic outlook and he's already been taught to expect the worst thing to happen during a mission, so having Morgan around while they're on a mission is the last thing he wants to do.
I've had people ask about Longshore, Crown Vic, and Cole Barker, so I'll make a blanket statement about that, too.
Some canon plots will still be in What Fates Impose, but only in that they make sense in my timeline. To wit, I thought Chuck and Sarah and Casey would have been handed the Mei-Ling Cho assignment, but it's doubtful they would be at the same sushi restaurant to meet Paine's poor first victim that Ellie tried to save, ergo Chuck Vs. the Truth never happened in Fates (which means Paine might still be at large, muhaha).
A general rule of thumb is I've been treating the episode airdate as a gauge for when the episode events happened, too. Crown Vic...has come and gone. It happened around the beginning of December, and now we're in January, so my apologies on that.*
That being said, we're still in January, and in the first season territory. Cole Barker, a second season character, is something like more than a year away, and who knows where the story will be by that time? And I think it's pretty safe to say that if things keep going the way they are, Sarah's probably not even going to be interested in that British piece of...beefcake.
Sorry for the definitive statements, I just wanted to let everybody know where we stand.
* There are two exceptions to this rule. One has already passed and was an author error, and the other is coming and will have an author's note explaining why at the time.