No, leave the nipples alone as there is no guarentee that the side you have modified will sit where it needs to sit.
You have to get new spokes and nipples, dont you? (the original thread shows a few broken spokes). You will have all the old spokes left over and you could make a "reamer" out of 1 of the old nipples.
Drill through the nipple (only enough to get rid of the threads, as the spoke will act as a pilot for the reamer to get the new angle correct). You can put flute(s) on the nipple with a hacksaw and file the nipple down to where the flute(s) resemble a drill bit (where the sharp edge is the highest part of the "reamer").