I cannot help you with M$ windows issues, or, to be sure, even GNU/Linux filesystems. I do not know how to remove the folders from your list. I found some files in the home directory (~/) like .conceal and at least one other, that may contain the encrypted versions of the files. Perhaps you can copy the files to another directory when the encrypted dir is open, then not worry anymore. If you have done this with all encrypted directories, you could delete those files (one of them is called "cache".)

I wasn't able to decrypt, but perhaps if that was working (it might be, but I was not successful the first few times, and now I am frightened to try) it would do something with the encrypted file and put the directory back in order. At least in a perfect world. It didn't work for me.

Good luck.