Reorganizing in lightroom, how does it affect Finder

I need to clean up and reorganize.  I've been moving folders, deleting folder,s moving images into different folders all within lightroom.  For example, I had a folder called 2016 in Lightroom that had 365 subfolders with photos.  I moved all the contents of the subfolders into the parent 2016 folder, and deleted the empty subfolders, from within Lightroom.  That folder resides on my external hard drive.  When I open finder on my mac, and look at that external hard drive, it looks like all the images are now under the 2016 parent folder (good), but the subfolders I deleted in lightroom are still there and contain all the images (bad).  Do I need to manually delete all of the subfolders and their content from within Finder also?  I thought when you move folders or images in lightroom it moves them on the actual disk?

Is there a way to do this type of thing in one step?  It's hard to remember to clean up Finder, plus I'm always scared to delete the wrong thing in Finder then in Lightroom I've deleted the source and it can't be found. 

Thanks!