Where to put 不 when responding in negative
As far as I can tell, the question does not require you to leave the 能 in the sentence. Since the 能 is already implied by the 可能补语 structure, the most natural way to solve your problem would be to leave off the 能:

你拿得来那本书吗？
我拿不来那本书。


By the way, to me it sounds more natural to move the object to the start of the sentence:

那本书你拿得来吗？
那本书我拿不来。


... but it's grammatically correct either way.