Most typically, Domain Trust issues come about when users are removed from the Domain's Active Directory without first removing them from GlobalSearch/GlobalCapture's security interfaces. When our system then goes to make authentication calls, it's matching a list of "Secured" users against the Active Directory, which no longer contains those users, creating a discrepancy. This discrepancy then results in the AD/DC flagging the application as "Untrusted" and not allowing proper authentication to take place.
Always take a full SQL Database backup before performing any SQL queries to alter or change your database.
In most instances, it will be difficult to pinpoint exactly what user is the cause of the Trust issue. It's usually easiest to completely blow out security and then re-log into the application as SSAdministrator or an SSAdmin and resecure your users.