The axle flip is sometimes done to provide more clearance when entering and exiting driveways etc. Sometimes people will add to the skids at the rear bumper or install real small guide wheels. I flipped my FW and give it extra consideration as the center of gravity is higher. I pay attention to the wind speed and direction also.
You can have the springs put back under the axle but try to mock up what it will do to your ride height. If you get under there and study it a little you will see that you will be lowering the trailer by this amount: the axle radius + the perch bracket (bracket that is welded to the round axle tube and rests against the spring) + the spring thickness. Your new center line above the spring will be those 3 things added together. So if your axle is 3 in diameter (1.5 R) + 1 inch perch + 2 inch spring= 4.5 in
Check your tire size also as they could have changed those too. I went from 15" to 16" when flipping so as to use LT tires instead of bombs.