Thanks I called Alaska and they were able to credit the miles immediately. It already shows up on my account.

The strange thing is that when I used the phrase "original routing credit", the first CSR I spoke with didn't seem to understand that I wanted the miles credited, so she contacted someone else within Alaska Airlines. The second person thought I wanted a travel voucher/discount code and was confused. But once I clarified that I wanted the missing miles, she said it was not a problem.