This is a good example of what happens if you just use specific commands (create this, do that, ...) without the proper understanding what is actually happening under the hood when you do this or that.
First question is, why are you doing that procedure you are describing, what are you trying to achieve?
Let me try to explain what is happening with these individual steps:
Step 1: Create a Folder Stack
You are creating a VCA Master Channel Strip (the new Main Track), and all Tracks in that Folder Stack (the so-called Subtracks) are controlled by the VCA Master Fader. Of course, you need a good understanding of the functionality of VCA Groups in general
Step 2: Flatten Folder Stacks
Two important things are happening when you flatten a Folder Stack. First, the visual grouping disappears (the disclosure triangle), and secondly, the Main Track in the Tracks List disappears. However, and this is important, the actual VCA Channel Strip, the VCA Master Fader does still exist in the Mixer (with any Level settings) and it still controls the former Subtracks, because (and that is also important) they still have their VCA Group assignment.
Step 3: Create a Summing Stack
If you create a Summing Stack at this point, you have to keep in mind the VCA Group assignments. Technically, you create an Audio Group, where all Subtracks are now routing their output to a specific Bus and the Main Track of the Summing Stack acts as the Aux Return using that Bus as its input. The functionality is the same as any Audio Group that you create manually with the only difference that the Tracks are grouped visually with the disclosure triangle. Keep in mind that you still have the VCA Group assignment you can use via the VCA Master Fader.
Step 4: Flatten Summing Stack
The procedure here is similar. The Flattening doesn't change anything regarding the routing of the Summing Stack, in this case, the Audio Group. The Aux Return Channel Strip and the routing of the individual Channel Strips still remain. The only two things that change are the disappearing of the visual grouping via the disclosure triangle and the removal of the Aux Track in the Tracks List, while the actual Aux Channel Strip is still there in the Mixer
Here is a screenshot how that could look like after all four steps. The 5 Audio Channel Strips are not visually grouped (stacked), however, they are still assigned to the VCA Group "Sub 1" and they are routed via Bus 1 to the Aux Channel Strip "Sum 1".

The Track List only shows the 5 Audio Tracks, but no Main Tracks for the Aux Return (Sum 1) or VCA Master Fader (Sub 1).
I explain all those details about the Track Stacks and their important differences with signal flow diagrams in my book "Logic Pro X - How it Works". That will give you a solid foundation to understand what is actually happening with all these commands so you can properly implement them in your Project.
Hope that helps
EdgarRothermich - LogicProGEM.com
(Author of the "Graphically Enhanced Manuals")
http://DingDingMusic.com/Manuals/
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