Asking a commitee to replace a letter of recommendation?
You can ask. They can say yes or no. But it might be an even better option to ask them if they will accept an additional letter that arrived too late to include. This respects everyone. 

If the answer is still no, then the professor who wrote the "replacement" letter might be convinced to send it directly to the hiring committee on his own initiative. It might be harder for them to reject it if he has a well established position that is known to them.