This can happen, when non-scrupulous devs 'deprecate' an older version of their app in favor of the 'new' version. e.g., you buy 'CoolApp' and in-app purchase features for it. But oh no, 'CoolApp2' has come out and 'CoolApp' is no longer updated for newer devices, so sorry.
Otherwise, an app, and its in-app purchase set remain available via a user's iTunes account indefinitely as far as I can tell.