I had Alaska arbitrarily cancel one just yesterday where I did that. I had two flights booked home the same day, different routes (an earlier one via Seattle) and was going to see if my business finished earlier if I could get home earlier. Here is what I got (and I booked it about 2 months ago).

“We have identified duplicate bookings which create “illogical itineraries”. This means that the multiple bookings would be impossible to use as intended. As we don’t want to limit seats for those who wish to travel, we have canceled your booking with the confirmation code:

If the incorrect duplicate was canceled, please contact our reservations team via web chat link or live chat text on 82008 for assistance.

Alaska Airlines”