It's possible I missed it, but I didn't see where it said how they came up with this strain of yeast. I was kind of assuming they used CRISPR or some other kind of gene editing to make it.

Regardless of if it was edited or selective breeding and random mutation, I do share those same concerns about how fast it might mutate and lose its effectiveness.

As far as it mutating into something harmful, sure it's a possibility, but the same possibility technically exists with any strain of yeast out there in the world, untold millions of generations of yeast have lived, mutated, reproduced, and died in breweries, bakeries, and vineyards since humans first started brewing beer and baking bread, and it hasn't gone horribly wrong yet. It's certainly worth being cautious about, and I'm certainly no geneticist to make an educated statement about it, but I suspect it's probably a pretty low likelihood.

The difficulty I see here is that it took the yeast not very long to mutate a beneficial effect, but it could just as quickly mutate away from that and even mutate something harmful.

That seems unlikely. The entire way it works is the yeast produces proteins that "look" like a virus to the immune system, causing a immune response. However that's the only part of of the virus in the yeast, there's nothing else that completes the virus. It's like... a steering wheel without a car, no matter how hard I mime swerving to run over a pedestrian nothing's gonna happen, because there is no car.

If the viral protein mutated it'd either A) still be recognized as a viral protein and generate immunity for a virus that doesn't exist, or B) generate a non-functional protein that the body would simply digest.