When you use Archive All and Add Tracker action, you may continue receiving more Messages for the associated TMail. When this list of Messages grows again in the Inbox, you can use Archive All and Keep Tracker, to keep archive all these (normal) messages while keeping the Tracker. (Please see About Trackers and Archive All and Add Tracker for more details.)
In Navigation | Message Flow, select the target Message. In Navigation | TMail Pins, you can also select Recent folder to see the list of all TMail Pins. Select the target TMail Pin that you want to use for Archive All and Keep Tracker action.
At the bottom of this list, you see an option of Archive All and Keep Tracker, as shown below.
Note that you only see the Archive All and Keep Tracker option if the Message or TMail Pin already has an associated Tracker. Otherwise you will see the Archive All and Add Tracker option for this Message.
Click on the small arrow and you see the four folders in the list. You have an option to keep the Message Tracker in its current folder, or to move it to another folder.
You can move the Tracker Message to other folders, if required. (Please see Move Tracker Message to Another Folder for more details.)