Regardless, I'm afraid this could turn into an Alias Smith and Jones situation. (Pete Duel died in the middle of a season and was replaced by Roger Davis, and that event is often attributed to the demise of the show with Davis being blamed for it.)
It's funny because I used to think I wanted a little bit of acknowledgement written into the show about it. But then in Sense8, we got it and it just felt awkward to me so I hope they just carry on as though everything is the same.
I won't be mad if they acknowledge it, but it would have to be done subtly, I think.
I thought Barney was exceptional as Mat, just perfectly woolheaded for me. However, I hope they don't even acknowledge the change, that would just make things worse, in my opinion. I don't think he left the show because he wasn't doing the role right, it must have been for personal or legal reasons.
Edit: And I do not think they would change the actors willy nilly.
Hopefully they'll show Matt trying to get the dagger back (cold opener for episode 1 season 2) Only to have Fain get it first and slip through the ways with Matt hot on his trail.
This would put things somewhat back on track for the Great Hunt