So if you delete a file in D:\$RECYCLE.BIN\ does it also delete the corresponding file in C:\Standalone\?
To my eyes, it looks like when a junction was created between C:\ and D:\, the files already extant in D:\ were simply moved to the recycle bin and replaced with symlinks. That should mean that the files in D:\$RECYCLE.BIN should be safe to delete. If files are in D:\$RECYCLE.BIN, they’re probably going to be deleted next time you empty the recycle bin, since the bin is really just a GUI for that folder anyway.