If a file in the srcdir is removed, exposing a file in the underlaydir, ikiwiki will not notice the removal, and the page from the underlay will not be built. (However, it will be if the wiki gets rebuilt.)
This problem is caused by ikiwiki storing only filenames relative to the srcdir or underlay, and mtime comparison not handling this case.
A related problem occurs if changing a site's theme with the theme plugin. The style.css of the old and new theme often has the same mtime, so ikiwiki does not update it w/o a rebuild. This is worked around in theme.pm with a special-purpose needsbuild hook. --Joey