How did you add them there, did you use a tweak tool?
You'll need to remove the key with the corresponding CLSID from here
HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\Windows\CurrentVersion\Explorer\MyComputer\NameSpace in the registry
Then simply move the directories you want to some location on D:\
Then create a directory junction from an elevated command prompt
Example for videos directory
mklink /J "C:\Users\<username>\Videos" "D:\Somedirectory\Videos"
This way Windows will still see it as it should be C:\Users\<username>\Videos but the data will be on the D drive