I just changed the transmission/hydraulic system fluid in my Ferguson TO-35.
There was a lot of water in the sumps, and I do believe it got in there just as Mike said above; through the two transmission shift lever rubber boots. I also noticed, a bit late, that there are two transmission drain plugs, and a lot of old fluid will remain in the system if you don't drain from both locations. I wound up draining and filling the system three times, and running the lift arms up and down several times with each change. In cold weather, I was having an occasional problem with the lift arms not dropping down, which made plowing snow a bit difficult ! I'm hoping that the fresh fluid will help. So far, the system operates normally again.
I bought some new aftermarket shift lever boots a couple of days ago . I've also started keeping a tarp over the tractor, something I haven't done for 34 years. I think finding all that water in the transmission scared me into finally covering the entire tractor.