We create a 3D markup in TcVis and in the Assembly tree we can see the Markup Layers. If we right-click on it we can choose "Send To Window". This will open a new window in TcVis that contains the Markup Layers and they are no longer display in the Assembly Tree.
If we close this new window the Markup Layers are no longer displayed anyway. This is true even if we capture the 3D Markup in a Snapshot and save session file.
In fact once we close TcVis and then reopen it if we make a new 3D Markup on different data it doesn't show up in the Assembly Tree or in a new window.
Solution
When you right-click on the Markup Layers and use "Send to Window" by design a new separate window appears and the markup layer is gone from the assembly tree.
When you do this the Markup Layers now act like a dockable window. You can see that if you go to Menu > View > Docking Windows it is now treated like its own window that can be docked or floating with the checkmark at the bottom of the dialog.
So when you do this and close your session and then create a new 3D markup, if this window was closed in your last session it acts no differently than say the Attachments or Window Properties windows.
If you want to get it back in the Assembly Tree, turn it on and then RMB and choose "Return To Tab". When you do that now it acts like the traditional use of the Markup Layers in the Assembly tree.
Notes