Due to Apple's position of not honoring warranties on phones damaged due to updates applied after a 3rd party hack was used, the fear of being left with a $600 doorstop has been prevalent. While I do not believe it is Apple's intention to break phones and they have said as much, it is a risk that any modder must take. The tool they will provide makes everything kosher again to make sure that doesn't happen:
We will provide you with a tool in the next week which will be able to recover your nck counter and seczones and even enables you to restore your phone to a Factory-like state.
After the update has rolled out and they have had time to work with it, they plan to issue another update to allow you to yet again unlock your phone.