What did he hear again, and what could he not see?
He heard the dogs again, and he could not see the lights.
If you're not going to post them as two separate questions, I would at least separate them with a comma.
For info, I don't know if you originally used "what could not he see" because you were avoiding the contraction "couldn't". If so, that is what might have led to the word order error.
What couldn't he see?
What could he not see?
Logically, you would expect "couldn't" to be extended directly to "could not" and for the words to stay in the same order, but they don't.