If a file in the srcdir is removed, exposing a file in the underlaydir, ikiwiki will not notice the change and rebuild it until the file in the underlaydir gets a mtime newer than the mtime the removed file had. Relatedly, if there are two files with different extensions that build a page with the same name, in a directory, ikiwiki will update the page whenever either changes, using the changed one as the source. But if that most recently changed one is removed, it won't rebuild the page using the older one as the source.