You should change both filters. One is for the hydralics; 3pt lift, front bucket, steering, etc and the other is for the hydro drive. The oil all comes from the same main sump and both could have manufacturing material in them. I had a good bit of metal shavings on the main drain plug magnet at the 50 hour change.
As far as the oil, my dealer said no need to change it at 50 hours but the manual suggests to do it and I figured it was better to do it then to later say ah @#$%. Besides, you may have some moisture in it from normal condensation.
As far as it being low now, highbeam mentioned the cylinders. They should be all retracted and Weldon gave you a good tip about checking with the dip stick. I always keep mine at the top mark of the dip stick. That way when working with the fel or bh, the level shouldn't go below the low mark. Derek has a good suggestion to check for leaks but make sure you check the oil level the same way each time.
My front axle had hydralic oil also. The manual calls for 90 weight gear lube. Five quart bottles will be the proper fill. Make sure you remove both drain plugs to drain it all. I'm just a stickler on service with all my toys. Usually makes them last longer.
