This is the official ruling, which has been worked into the marginalia in what will be the final text:
It's much like boxes that you don't get access to when someone attacks you with something that satisfies The Catch. The boxes are still there, still numbered as they're numbered, still marked; you just don't have access to them when you're in the other form.
So, say you shapeshift into a form that gives you a 5th and 6th stress box, and you get hit several times, and hard. One gives you a Mild Consequence and another gives you a mark on your 5th stress box.
Then you shapeshift back. You can only access stress boxes 1 through 4, but there's still a X mark on your 5th box that'll be there when you shapeshift back (or will clear out once you get to clear out all your stress boxes normally).
The mild consequence would still hang around too (and this is where you see the Alphas still carrying over their wounds from their wolf forms).
"Hey, what if my form has an extra mild consequence slot?"
Similar logic. It's still there, and still occupied (and still taggable!), you just don't get to access it for its benefits.