I can't say that I have been in the exact same position, since I don't run an affiliate program, and I have back-ups of my back-ups (sometimes a little paranoia is a good thing), however, I know I freak when I can't access 3rd party data (stats, etc), even for a few hours or so.
You seem to be maintaining quite good under the circumstances, while you work to rectify the situation, as well as keeping everyone informed about what is going on (it's always best to be out front on stuff like that).
If you ever get tired of running your web site, FEMA could use you - and you would probably do a better job.
ADG Webmaster