I have on the same dashboard a few searches, all scheduled, out of which half are not actually saved (when opening the dashboard some of the panels appear immediately with a "... hours ago" while others's search is run only at that time).
They look similar in the configuration. For instance this one is scheduled & correctly saved
It is possible to use a search in a dashboard that is not in the saved searches list. If you created the search within the dashboard, or altered the search parameters within the dashboard context and did not change the original saved search, then that search would not be shown in the saved searches list.
Also, your missing search may be in the $SPLUNKHOME/users/username/appname/local/savedsearches.conf file not in the $SPLUNKHOME/etc/apps/appname/local/savedsearches.conf file.