As it is common for many people living in several locations, I have several iTunes accounts. It happened I purchased (well, it was free, but technically it's the same) an App from the Swiss App store which has now been removed. However, the app is available in another country's App store for which I have an account.
Now, when I am connected to this App store my iPod detects an update of the application (from a different country's App store from which it has originally purchased). When I try to update it, it asks me again the original country's App store account password, which I provide. But the result is that it bounces back to the other App store and tells me that the app is no longer available.
Currently, I don't see any workaround for this problem.
Of course, it is in general very annoying having to switch from one account to another for updating the apps (including selecting the different iTunes stores and wait that everything loads).