you can do it with a provxml, add this to "pre XML" or "post XML" section, depending on needs, on the "cab information" page in wincecab manager
Code:
<characteristic type="FileOperation">
<characteristic type="*full path of file to delete*" translation="install">
<characteristic type="Delete">
<parm name="ForceDelete" />
</characteristic>
</characteristic>
</characteristic>