I think you are using Folders when all you need is Collections (and, occasionally, "All Photographs" from Catalog).
Folders exist on your hard drive. That's where the raw images are saved. When you work on an image in LR, or Edit it in PS and return to LR, what you do with it exists in the Catalog and all appropriate Collections, but it isn't saved back to the hard drive unless you explicitly choose to Export (when you typically end up with a tiff or jpeg, depending on your choices in the Export dialog).
I never touch "Folders" in LR after I have imported a raw file. Once I have processed the file in LightRoom, if I exit LR, the instructions for processing it are saved in the catalog (and I always back up the catalog on exiting). If I have finished processing a file and I want a jpeg for use on the web, for example, then (and only then) do I export the file as a jpeg.
I hope this helps.
So I have never found a reason to look at "Folders" at all in LR.