Here is my experience:
I have 2 cards from a 2bm on Dec 12. I am keeping one card just in case I need to manufacture spend and build more miles on Alaskan, but two cards is redundant.
Last night, as Day Sixty was looming, I did three chats and a phone call with the goal of "get the AF waived or bust!" Well... I never got the AF waived. I suppose I could have closed the card (and lost the CL) but instead what I did was to change the card into a Better Balance. They told me that the AF would get credited back eventually.
Interesting data point, the Senior Account Specialist on the phone who changed the card type for me actually told me (without me asking!) "Don't worry about your Alaska miles! They are all safe! They are staying no matter what you do!"