I did this a while back to change a Duncan Seth Lover from long leg to short leg for the same reason. I used a Mojotone short leg baseplate
If your pickup has a cover you'll have to desolder the cover from the edges of the baseplate. Then you basically unscrew the four little screws on the bottom of the baseplate, pull it off and screw the new one into place. It's really not too complicated, especially if your pickup doesn't have a cover.
Some people say that the baseplate material affects the pickup tone, but I don't have any personal experience with that. Baseplates are generally either nickel-silver or brass. Seymour Duncan uses nickel-silver baseplates, so stick with a nickel-silver replacement and there shouldn't be any major change in tone.
Finally, Seymour Duncan offers what they call "shop floor custom" pickups available through authorized dealers and I'm pretty sure you can order a short legged 59' as a shop floor custom this way for little to no up charge. I haven't ordered a shop floor custom myself, but I've heard of a lot of people doing it through Mike's Music Shop aka banjomikez on Ebay. I think it would be worth shooting them an email to find out as it would mean one less thing to go wrong and it wouldn't void the Seymour Duncan warranty.