Let's take a step back:
1. Verify that all Automatic Action Notifications are un-checked in ClearContext > Options > Preferences > Misc.:

2. Click Reply on a message.
3. In the Reply, change the value of Orig Msg to Delete or File to Topic:

4. When you send the reply, you will receive this dialog:

ClearContext will remember the last value set for Original Message, so the next time you reply you won't have to set the value to Delete again.
That's what you're looking for, correct? Does it work this way for you? If not, go to ClearContext > About > Email Support, send me the data in that email along with a screen print of the Misc preferences tab and a screen print of a reply before you send it. Thanks.