Sadly that is not the case for all apps. When Stanza went, it went from purchased as well. There are probably others but thats one I know of because I still use it for downloading books, and then being able to save them out via itunes. I don't have any other readers I can do that with (suggestions anyone?)
Apart from Stanza which won't keep working, I also have Bookworm, Azkend and Wallet. I've written to Acrylic software devs to get Wallet updated (they did it for the Mac version) but if they dont do it, oh well, I have got my alternative in place. I dont much care about the games, I have old devices I can use if I really want to play them.