There are 2 definitions of "protect" used around these parts.
If you are asking if they will proactivily take care of you, I think tennis is likely correct. Only if a bunch on the SN-TPE will miss TPE-USA. And even so, they might not notice you (but if you ask, I think they would likely take care of you).
If you mean will they allow you to rebook on the next availablity flight, then yes. They should do this. They have no rules on such (that I know of), but it would be consistent with how they work in other cases of missed flights.
Fortunately they never learned the US carriers ploy of trying to rape those with travel fails.
And I do not do checked luggage, so can not help you there. I would think they would through check though.