You can disable reputation approvals for individual files.

If you create the exception before enabling reputation rules on your server, it prevents any approvals by reputation for instances of the file. If you create the exception after enabling reputation rules, the reputation-approved file will revert to unapproved (both globally and locally) if no other approvals apply. If the file was already locally approved by some other means, however, (such as publisher approval or a custom rule), it will remain locally approved.

When you disable reputation for a file, it affects only that file, even if it is an installer.

To disable reputation approval for a file, open the File Details or File Instance Details page for the file and in the Advanced menu to the right of the main page, click Disable Reputation Approval for this File. Reputation approvals are disabled for the file .

The Advanced menu with the Disable Reputation Approval for this File highlighed

To re-enable reputation approval for a file, open the File Details or File Instance Details page for the file and in the Advanced menu to the right of the main page, click Enable Reputation Approval for this File. (This choice only displays if reputation has been disabled.)