First thing to do is to make a back up of all your user folders contents on to an external drive preferably. Then if anything (will?) goes belly up you will still have your data. Have a read here , especially option two.
You should then be able to delete the folders on the D drive and start again.
My setup I don't use a redirect switch. I simply create folders on the D drive. Download2 for instance and use my browser to change the destination of downloads to Download2 on the D drive. If I've downloaded a music file I can then check the file is ok and copy and paste to my music2 folder on the D drive. Photos, etc. you can save the same way. If I've downloaded a program installation file, say, Ccleaner for instance, I'll create a ccleaner folder (D) and install to it. The shortcut on your desktop still works. It's all manual but easily done and takes no time. That leaves Windows in a default state with no redirecting switches so if I need to reinstall or upgrade Windows both drives are independent. That's my theory and it works for me.