Surprisingly, the filament-changing process was smooth and simple. Once we paused the print, the Makerbot screen walked us though the process. Once un-paused, the print continued as it nothing had happened! The most interesting part was that, when paused, we got a message while the code wrapped up a few layers, getting to a good stopping point. Smart.
A quick Google search of "switch filament mid-print" will uncover many people who use this technique successfully to acheive some pretty cool results. Interestingly enough, we've read that "MakerBot has invented a new type of process which, if it works properly, will allow 3D printers to change build material mid print. They have filed a patent to protect this solution over a year and a half ago, but just recently was it published for the public to see."
Another tool in our toolbox! :)