Check news/announcements, they just finished the second step of the SAN migration - now the SAN is serving files.
What happened in your case should fix itself though - the initial sync had a lot of files to transfer, which means during the transfer the ones that were created and/or modified didn't get their changes moved over.
They're running a second sync now to catch all the new and modified files and copy them over too - news post is estimating about 1 day maximum depending on when it gets to your account on the server. If it's still not fixed this time tomorrow, post back and we'll see whats happening. For now, it's not the -best- thing to happen, but it is already working to fix itself at least