Apologies if posted elsewhere and not directly related to the website, but I had this experience last week in relation to the changes.
I took a domestic flight in Australia on VA, which was booked by a colleague so I wanted to add my VS FC number to the booking at the check in desk. Gave them my new lifetime FC number, and they were unable to add it to the booking, computer kept saying no.
Was in a bit of a rush so didn't have time to dig out the old number and try that, so now have a missing miles claim to make. Based on what I've read in this thread, that should be fun...