Going back to your post #1, Windows was reporting "Data error ( cyclic redundancy check)". When you tried to run checkdisk, it refused saying it can't run on a RAW drive. This problem sorted out by itself ( I still don't know how) and you were able to run check disk and it ran to completion.Partition Wizard shows that the GPT structure is fine and so it is not a partition related problem.Now Lucid Puppy also says error for Source file Input/output error.
As one who has been dealing with data recovery ( though not a data recovery professional

) I can only visualise it as due to bad sectors. But in this case it appears that I may be wrong. The problem of your inability to access the lower tier folders can be due to the way you had created the folder structure and named those or some corruption that had taken place in the folder structure. I may not be able to deal with such a problem.
To clear that bad sectors are not the cause , you may run SeaTools for Windows and check the health of your drive.If it does not report any problems with Quick Test and Extended test - which of course will take a long time - then it squarely revolves around the folder structure/ corruption and I shall pass it on to other experts to deal with it.
Let us wait and see what other experts have to say.