When running /opt/quest/bin/vastool list users-allowed, the users are listed and the following warning is given as well:
"WARNING: This list contains only locally-cached users."
The command tells QAS to list users that are allowed to authenticate to that system. It will do that and the warning is there to let you know that this is the list that QAS knows about according to what has been cached since it last was updated.
Running vastool flush won't change the list unless there has been a change in AD. And even then there will be cases when replication hasn't completed in AD and it won't have updated for every user, and so on.
This is nothing to worry about, this message is perfectly normal.
Running with the -f option ie. /opt/quest/bin/vastool list -f users-allowed (available in 4.0.3 and above), will enumerate the groups in users.allowed to show a more accurate list.