If I understand this correctly, you have the following problem: But none of the answers were really that great, nor did it really pertain to my particular issue.
Yes, I know there was another question on SU about 'windows folder with millions of files not responding'. I've tried optimizing the folder for Documents, (I read that reduces load time in Explorer) I tried using Folder Axe (a folder splitter) to break down the root dir into more manageable pieces, but it lags up when choosing that folder to work with. It took almost 3 days to run both programs, and now, neither Windows Explorer or a minimal file manager in Puppy Linux can load the directory fully. Little did I know, DiskDigger has a file destination name limit, so I was forced to use the root directory of my already quite full external drive. I used Recuva and DiskDigger from a Live environment to copy the files to my 3TB external HDD. I have a client that knows nothing about computers, and did a format and reinstall from the recovery partition of his old AMD Athlon II X4 desktop running Windows 7.