I've been hit with this too. My apps on the website are completely gone. The orders are still there, thank god. So if google ever actually try and help I can prove I bought them.
All I did was clear cache and data in the play store on ICS because I couldn't download updates. Did they change clear data so it wipes EVERYTHING server side?
My playstore on my ICS xoom has a completely blank "my apps" page. If I try and update my apps it asks me to pay.
My nexus one on GB still uses a really old version of market (I froze the updater some time ago) and that's working fine at the moment. I can do updates ok too.
On my xoom I unistalled updates to pre "play store" re-brand (so plain old android market) and it shows all my apps and lets me update them without asking me to pay again. Next time I open it, I'm back on the play store with no apps listed in "my apps". So I uninstall updates again next time I need to use it. There doesn't seem to be an updater to freeze any more.
I daren't try buying any new apps in case that messes it up even more.
As a short term workaround try using an older version of the market. The one that works for me is 3.3.12.
I've tried going back to a nandroid from a couple of weeks ago, didn't work. I've wiped, flashed, market doctored, everything I could think of. No help. This is definitely server side.
I've sent emails to google but they haven't replied. I sent a few because there wasn't an option for "you deleted everything on my account for no reason."