I too had to replace the bathroom floor and entire rear area of my 94 T-2670.
As for the toilet flange after you remove the screws it is threaded into the top of the holding tank.
Here is link to my post on floor repair.
As you can see I had to remove the bathroom vanity and the rear lower bunk.
The damage in my TT extended down the center all the way to the couch.
I removed all the damaged wood and wet insulation and ran a fan to get good and dry, treat any mold areas with a solution of bleach and water to kill the mold.
I used a Marine grade plywood and installed a laminate floor over that.
Hope this helps and good luck.