Wow, I had no idea why I have two pieces of plywood on my bathroom floor. An older home and I have to do exactly what this thread is about...replace the toilet and a section of the flooring. I cut out a slice of the floor and was surprised to find two pieces, one about 15/32 and the other was 3/4.
I am nervous about what I will find when I take the toilet off. I am not exactly a "handyman" but I can do basic stuff. I think I did something like this about 20 years ago but I had help. lol. This will be an adventure. I have all the materials, except sealant for the vinyl floor tiling which I forgot to get. I just want to make sure I can replace the section of flooring and have the toilet level and stable.