Images not showing in Media Library on WPMU - file path changed for all sites

All sites on my WPMU network are showing broken images in the Media Library -- and the file paths have all been reset to /files/ instead of /sites/xx/ (eg. /files/2016/05/pma-logo-70x70.png).

How can I change the urls back to their proper paths? Image are showing up on the public site, but not in the Media Library.

I'm suspecting since this is a global issue that there is an .htaccess problem. Or is it a database problem? I'm OK working with PHPMyAdmin if needed.