I am running Nuke 7.9 with the subBlack theme. The right blocks disappeared with me too. I don't run the patch referenced above, but one small section out of the linked readme returned my right blocks.

This:

In Themes:
if ($index == 1) {
to:
if (defined('INDEX_FILE')) {

It's not clear in the readme, but what that means is that you need to edit the "theme.php" file included in the root directory of your theme. Aside from that, change the text exactly as it says and you should be working fine afterwards.