I received this from e-miles about an hour ago:

Hello XXXXXX,

I have heard back from Alaska Airlines regarding the missing redemption points from our members.There was a system problem on Alaska's side where eMiles redemption request did not process correctly. That is the reason why our members weren't seeing their points in their Alaska accounts. Alaska re-processed the files and my Tech Team has advised that they've received confirmation that the miles have been successfully deposited.

Thank you for your patience,
eMiles Support