Sounds like something that may not be legal for them to do, depending on your state's warranty laws. Check with your state attorney general's office.

 

Seems only fair to let the shop that allegedly did things wrong have a chance to look at it and make good on their mistakes.

 

If a tractor under warranty breaks down in the field, most manufacturers will not cover transportation costs. If you move or another dealership opens that is closer, that dealership might decline to work on your tractor because you didn't buy it from them, even though they sell the same tractor for the same manufacturer. Why? Because warranty works for non customers pays slower and sometimes less. Because they make people that bought tractors from them the higher priority. Both reasons I mentioned involve money.
None of that seems very fair to the person that shelled out 30 to 50k for a small to medium duty tractor, but that is the way it works.
Personally, if a dealership made a 5K mistake on my tractor, the manufacturer was informed and wasn't stepping in to make things right, being fair to that shop would be the last thing on my mind.

 

Warranty work typically ends up being the manufacturer (John Deere) will provide parts free to (Dealership) but usually still has to provide a set rate in costs for labors involved. I'm guessing JD in this case wants it to go back to original place where the repair was made in order to negotiate repair costs. Payments have already been made most likely so JD will probably try to offer a reduce payment to dealer for the repair since it was not done correctly in the first place.

Definitely if possible get documentation from the other dealership indicating the original repair was done incorrectly because most likely they will try and say it was owner related to get maximum payment from Deere for the warranty work.