Do a double oil/filter change. You won't be able to drain it completely, but you can drain from all the connectors you can get to. Just be carefull when you start the system up again. Hopefully there haven't been done any damage to the system.
Do you know the reason for the water in the oil?
Maybe some hard rain on some trash sitting around the fillercap? Dont know the Deere combines, would they have a water cooled hydraulic cooler? are you loosing coolant? have you used a pressurecleaner around the fillercap/breather?
For sure it would be nice to know where the water is comming from. Otherwise you waste a lot of time/oil/$ and it is a nogo for the hydraulic system on the long haul.
Take the time to investigate the problem...