See the picture below. If a window is “racked,” dimensions A B and C will all be the same. Therefore if you order a window that is A inches x D inches it will not fill. The new window will come out perfectly square and will not fit into this hole. So it is not merely enough to measure the window in three different spaces, but you also have to measure the diagonal to make sure the hole is square.
I realize this is an extreme example but beware, even a small difference will wreak havoc on your new window. It may fit in the hole, but when it comes time to adjust it, you won’t have any room for adjustments and will be unable to get the window to work properly. Always measure the diagonal and make necessary adjustments with your measurements.
You don’t need to do anything with this measurement, in fact throw it away after you’re finished so you don’t mix them up with something important. You simply need to make sure the dimensions are the same, to verify that the window is square. If not, you will need to make your measurements smaller for the new window to fit into the existing opening.