Out of curiosity, why do you throw away the wrong file?

Anyway, in the search result display, you can click on "Show settings" and change "Ignored files are not displayed" to "Ignored files are display marked". They are then grayed out.
If you want to download the files again, not just see them, you also have to remove the corresponding entries from ~/.gtk-gnutella/done.sha1 and/or ~/.gtk-gnutella/done.namesize. If you cannot figure out which entries are the correct ones, just remove these files completely. In any case, be sure that you terminate gtk-gnutella before fiddling with these files.