Well, regarding the initial thread question "The rules around what gets replaced and what gets added when reuploading a folder structure", the answer is pretty clear from this thread. We will have to take into account that if we rename a query and reupload, the old query will still be there.

A minor gripe in the grand scheme of things.

I am glad I got all the other critical pieces together. I can export my structure, I can modify and build it using a script, then I can upload it using the commands you gave me.

That will do :)

Thank you for all the help :)