Thank you all for the comments.
crelf: I don't think I understand the scenario you're describing. In this case, API 2.0 has updated a .ctl file that API 1.0 also uses, which means that API 1.0 will be broken when loaded into memory unless its references are automatically updating or disconnected. Is that what you're describing? That seems like automatic mode is helping you in that case.
asbo: This is another scenario I don't understand If the typedef reference is manual, then it will break when the typedef type changes. If it is disconnected, then it seems more useful for backwards compatibility. Were you perhaps thinking of disconnected instead of manually-updated?