I believe I have that same deck and deck adjustment system on my 05 - 3100. We only have about six hours on the machine so I don't know much about it yet, but that deck height system you are talking about doesn't seem to function quite like the instruction manual says. You are suppose to be able to lift the deck to #6. Mine won't go there at all. On my tractor, the entire adjustment of the deck lowest (where I mow my grass and the highest (about 5 on the scale) is only about 2 inches. I think to repair your situation, you are going to first take the deck off the tractor. Don't try taking it off the RH side ....it won't come out that way. There is a special procedure which needs to be followed to remove the deck and it involves adjusting the parts that make up the deck height system. If you don't have the manual for the machine, it will be hard to figure it out. I have the manual and even with that it took me an hour to figure out how it comes apart. Once you have taken the deck off and put it back on once the correct way it is very easy (except that the deck weighs almost 300 pounds and is a beast to handle by yourself. Once you have the deck removed, look up under where that deck height adjustment is located. I think what might have happened to yours is that you may have turned the adjustment level too many times in one direction and caused the adjustment screw to fall out of the lift arm.
Good luck!