That is exactly my issue Some are still there (I got CowLick back) and some aren't (WPCentral and glƏƏk!)... I am still waiting on MS' response.
For me I've lost all the paid apps that went on free sale for a short period. I had connectivity issues with the WPCentral app, uninstalled and zip......nothing in my history. You go to the main app, it asks you to buy. Now I lack the WPCentral app on my phone which is kinda emptiness for me cuz I was too addicted and used to it. Still waiting for Microsoft to give me back my purchase history :'(