Yes, they can be swapped, just reverse the procedure on the page below:
- http://www.4x4wire.com/toyota/tech/autohub/

When the auto hubs work properly, you should have no extra drag or drive train wear as they should unlock once you are in 2WD. Main issues with them is that they can act up and either not lock when you need them to or they can unlock when they should not. For example, if you get stuck and the front tires can turn, the hubs will not lock automatically, since they need the wheels to turn to engage the hub. They can also unlock in reverse.

With manual hubs, you have full control, they are locked when you lock them and unlocked when you unlock them.