In my experience CC will only clean known temporary data on the C (system) drive, and it will not by default delete any user files. The only way I know to delete user files on a non-system drive is to specifically include the folder/files with Include statements (but you don't have Custom Files/Folders checked), or to run an erase drive command from Drive Wiper. This is assuming that the D drive contained user files instead of, for instance, a redirect to hold only temp internet files.
There's no way to undo file erasure done by CC. Whether anything can be recovered from the D drive depends on what's actually happened to erase the files.