I finally found a way to fix this for the specific project I was working on: in module_form_alter I added the following: -
global $_domain; if (isset($_domain['domain_id'])) { // only display domain primary links $menus[domain_conf_variable_get($_domain['domain_id'] ,'menu_primary_links_source')] = $_domain['sitename'].' Primary links'; } if ( isset($menus) ) { $options = menu_parent_options($menus, $form['menu']['#item']); $form['menu']['parent']['#options'] = $options; }
This limits the menu options to only the main link menu of the current domain that we wanted.
Thanks to Fabian , who pointed me in the right direction before .
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