I suspect you are looking at two different folders, perhaps downloaded in different ways. From your Finder, when you can see the version with the subfolder you want, try double-clicking on the .RProj file to get RStudio to launch. Once you're inside that version of the project I think you'll see the subfolder.
Thank you for your timely and accurate solution to an embarrassing oversight on my end. Indeed I had recently migrated to a new computer and on your suggestion confirmed that the root directories were slightly different.