I'm using Sitecore fast query to get results. But I'm not getting any results if I use the query in master db, I tried running it in XPath viewer as well. But I get the results for Sitecore query. The same fast query works against web database.
fast://#sitecore#/#content#/#Something#/#Something#/#AU#/#Website#/ancestor-or-self::*[@@templateid='{463D7680-BF52-49DF-B7D5-88E97416A1FA}']/Configuration/Navigation/Footer Bottom Right/*
I still really don't understand what is the cause of the issue, But cleaning up all the databases solved the issue.