I would say yes, if you are experienced in sewing. But if it were me, I would order some 1.1 oz. sylpoly from ripstopbytheroll and make a copy of the annex and put a zipper in it. And the stove jack if I wanted.
Then the integrity of the original annex remains. And you now have options. I had a paratarp with annex and used it for awhile with stove. I then stopped using the stove since I was hunting archery. Then the annex stayed home after it seemed like it was not necessary unless weather might be a problem.
Just my two cents.