And you misunderstood my post.
Firstly all alerts are logged, so none are unknown.
Secondly, in the end CIS either blocks (denies) or allows. There is nothing else, silent time-outs or anything. Just block or allow.
If a process has frozen/hung when CIS's alert disappears, then the process would have done that anyway because that's how it has been coded (exception handling) and it missed CIS's default "block" when the alert disappeared. This probably happens because the process didn't expect to have to wait for resource/device that it had been temporarily denied (silently denied, not to be confused with silent time-outs, etc..) to it by CIS. In short, nothing to do with the alert being visible or not.
If you're a coder, this is why CIS D+ is extremely useful for exception hardening/testing.