There's a photo in that article that shows the problem: the flip-tab sign that has space for four numerical digits. I was thinking they could just switch from 0-9 to 0-9A-Z but that photo showed why that would be a disaster.
Plus any solution has to be approved for use worldwide.
Fortunately the two-digit IATA codes have already switched to 0-9A-Z (e.g. JetBlue is B6) so allowing constrained airlines to use two codes should work fine.