Yeah, she recently gave birth (within the past month or two) so she probably left right before it happened. they've played it off like she's been mad at Barney b/c of the joke. she'll probably be in at least one scene next week since it's the season finale.

From EW.com:

'HIMYM' scoop: Stella's the mother! Or IS she?

I defy you to find a single fan of How I Met Your Mother who isn't asking themselves exactly that question in the wake of last night's humdinger of an ending -- which seemed to strongly hint (if not outright reveal) that Sarah Chalke's Stella is the show's eponymous mom. Unfortunately, only two people on the planet know the answer. Fortunately, I just got off the phone with one of 'em --executive producer Carter Bays!

Is Stella the mother?
CARTER BAYS: I won't say whether she's the mother or not, [but] we were definitely very careful in the wording of the narration. Obviously, we're not going to say, 'Okay, here she is! Show's over."

Was it an intentional fake-out?
BAYS: Nothing's a fake-out on this show. We established very early on that this is a very windy, twisty story, and the message of the show is there's a ridiculous series of events that has to happen before this guy meets the woman he marries... I will say this about the next two episodes: Everything will be made clear and it will move the ball forward.

You certainly got people talking.
BAYS: We freaked out a ton of people. We've never really kept a big secret from the audience. And what secrets we do have we usually tell people and there are usually spoilers floating around. And this kind of felt like, "Let's try and do something that takes everyone by surprise and really blow people's minds." And I think we did it.

What kind of reaction have you been getting?
BAYS: It seems to be split 50/50; some people loved it but a lot of people really hated it. And I certainly don't want to tell you that I like it when people hate my show, but knowing where the next two episodes go, I feel like those are both legitimate reactions and both what we were going for.

Does the yellow umbrella belong to Stella?
BAYS: I can't say one way or the other.

Can you give me a preview of next week's episode?
BAYS: We'll reveal why Ted running into her again is such huge moment. He already ran into her once before and didn't do anything, but this one has more meaning and we'll find out why next week.

Is it your plan to hold off on confirming the identity of the mother is until the final episode of the series?
BAYS: That's always been the plan, but obviously we have a lot of options at our fingertips.