Upgrading projects from one version to another has never worked, in any IDE for any compiler for any system, ever in history. Create a new project.
I suspect your problems may be related to newer CW versions using an include called <derivate.h>, which in turn points at a register map relevant to the CPU used in the current project. Try including this one instead.
If everything else fails, copy the MC9S08AC16.h to your local source directory, then include it with #include " MC9S08AC16.h" rather than #include <MC9S08AC16.h>.
Though of course the best option is to write your own register map, so you aren't stuck with Codewarriors crappy one, which doesn't even follow the C standard.