Saved Searches are the nodes in the navigation tree to the left in the UI.
Hmm .. X1 removes from the index files that cannot be found during a re-scan, but there is a logic which prevents this for files located on a network share, as the network share may be temporary unavailable... One possibility would be if the network share appeared to be accessible, but the files were not ....This needs more investigation.
We had reports of similar issue before, but we were not able to reproduce it .... can you go to your data folder and look for a file named SharedCache.xml - stop both X1 UI and the service, the rename the file, and then run X1 again - (you may have lost the "Last Indexed" info for the scenners, but it will be populated again soon), and now try to change the schedule for the different scanners and see if they stick.