Some people don't get this, so i will try and explain in simple terms.
I will use a farmall example, just because i know them.
With a little bit of work, a farmall m engine could go into a 560 or viva versa.
A super m makes 47 hp at a rated engine speed of 1450 rpm. If you wind it up, it will make 53-55 hp at 1800 engine rpm.
now a 560 tractor is set up so that the engine turns 1800 rpm to get 540 pto. If you put the super m engine into the 560 tractor and put it on the dyno, the engine would turn faster (1800) to get a 540 pto speed, and you would read 53 hp on the dyno.
Put that engine back into the super m tractor and put it on the dyno, and it would turn 1450 to give you 540 pto and read 47 hp on the dyno.
You are basically doing the same thing. You are changing the engine rpm in relation to the pto rpm.since in the tractor world hp is measured based on pto rpm, changing the engine input speed will give you a different hp reading.
If you were to use a pony brake belt pulley dyno, you would see no difference on your John Deere because the pulley speed doesn't change with the gearing change.