have a question,

would comodo cis generate firewall alerts to a file already on the trusted files list of cis?

Depends on your setting.

For the firewall i would recommend to use custom mode. And no automatism.

It will not generate an alert. But when a sandboxed application would start that trusted application the trusted application will get sandboxed and you would be alerted.

Custom mode generates an alert for me with trusted files.

When you have no rule for application which are trusted files you will be asked. When you make a rule in Application Rules for a program you won’t get Firewall alerts in Custom Mode.