Might be able to look at this more than one way.
I bought new tires at AT last Oct for one of my SUVs, and I bought the certificates along with them. In Dec, > 6k miles later, I got a large screw in a tire and went to AT to have it taken care of. I walked in and explained I'm losing air because of the screw. The counter fella looked up my info on the pc, then sent out a coworker to see if they had another tire of same make & size. I told him to just remove the tire and plug it. Now instead of looking at my vehicle, he wanted to make sure they had a replacement first just in case it's non reparable once they break down the tire and inspect for damage safety wise bla bla bla
They plugged the screw damage since it didn't cause any tire damage, And they rotated & balanced all tires. The fella was telling me even if it went flat and I drove and ate up the tire, the certificate would replace it, no charge. Don't know if I believe all that.
In your case, no certificate, if they pro-rate the tire, then the percentage rated should be the difference of the tire. But, since you now bought the certificate, you might want to look at all your tires (4 on the ground) are now fully covered, even if the mileage has the tires mostly worn out. Not all sure, but that might be a consideration that all have full coverage.
I know if the tires are lets say 75% worn, getting one replaced would no longer provide you a full match set as far a wear goes.
I don't know as I say, just speculation on my part - but I had no hassle and they were ready to put a new tire on my vehicle no questions asked. He just wanted to make sure they had one for me just in case it needed it when they got to inspecting it.
Just my experience. Only negative is I wish they wouldn't put that shiny stuff of the tires when they remounted them, but I forgot to tell them not to in this visit. It was the day before x-mas and I was running around like mad and a lot was running through my mind, and of course I got screwed just to change my day.