If your franchise is already started, they won't be added there. You need to create a new franchise with an official roster from September 25th or later. The rosters released September 3 and 16 doesn't have the Senators alternate jersey. I assume with shared rosters, it will matter which official roster they are based on, if the jersey will be in it or not. But the point is, you need to create a new franchise to enjoy the Sens alternate jerseys.
It's really a bummer it works that way, because whenever something like this happen, unless I've missed something, starting a new franchise is the only way to access the new content. Would be great if it was possible to download jerseys and stuff within a franchise mode at least.
Last year same thing happened to me, but when they added real coaches. I was three seasons in (I play all games, so that is plenty of time invested) and to reset my progress to get the coaches didn't really feel worth it. But changing coaches for all teams is something I understand that it can't be fixed mid franchise. Adding jerseys however, that feels like something that is reasonable to add.