Changing the size of the flipper is a 100% reversible mod, so I say go for it if that's really what you want to do. If you find that you don't like it, you can always change it back.
To do this mod correctly, as zacaj mentioned, on each flipper you will need to remove the shoe-and-shaft assembly (with the 2" shoe) and replace with a shoe-and-shaft assembly that has a 3" shoe. And, as PinballAir mentioned, be sure to save all old parts and, ideally, store them in the machine.
The shoe-and-shaft assembly is removed by loosening two set-screws on the flipper crank located under the PF, and pulling the flipper bat and shaft out from the top of the PF. In theory that's easy to do, but in the real world you can run into a couple of complications. First, the set-screws may be difficult to get loose, and second, burrs on the shaft created by the set-screws cinching onto the shaft can make it difficult to extract the shaft from the plastic bushing.
When you remove the original shaft and shoes, be sure they are marked as to which one is the left flipper and which one is the right flipper. That way, if you ever want to re-install them, the existing set-screw indentations in each shaft will help to get the shaft back to the original factory position. If you keep the plastic flipper bats attached to their respective shoe-and-shaft assemblies, then you'll know which flipper goes where because of the lettering on top of the bat.
- TimMe