I'm in the midst of replacing the front half of my floor for the same reason. The floor on my 06 is 1/4" ply on top, 1.5" Styrofoam in the middle, and 3/8 ply on the bottom, all glued together. The bottom ply was much worse then the top, you should be able to tell by feeling the underside. It is supposed to be hard as the plywood is directly under the lower plywood sheet, mine felt like mush, which is what it was. I just finished gluing the top plywood in yesterday, and I'm doing the easy end of the trailer. Had to remove all the cabinets, stove, sink, and dinette, as well as a half wall at the front bed, and the water heater. I stopped at the fridge as the floor looks okay, at least on the top, from that point forward. A lot of the electrical and plumbing has to be dealt with too.
Had to remove the frame bolts and most of the lower trim to allow me to jack up the box so I could slide in the lower plywood, it needs to support the side walls and I didn't want to piece it in. Probably should have removed the door too but I didn't as I don't have covered storage.
I hope I have taken care of the original source of the water but really am not sure, but half my time was resealing everything seem or hole I hold find. It looked like water gets in pretty much anywhere there is an opening. From the storage access doors, the front bunk, doorway, and even the hole the water heater goes in. Getting my 1st good rain since I started at the moment so I'll see what it looks like in the am.
Good thing I retired a month ago as I have at least 2 weeks time into it, also about $400 and I have yet to buy replacement flooring. Having a Dremel tool to cut in corners is a must. I also had to cut more then a few screws and staples.
If you're handy and have the time you can do it, but it isn't easy or quick. If I'm lucky, I can remember how to piece it all back together (took a lot of pictures as it was disassembled), and I won't end up with too many extra parts.