If you copied everything from the H: drive to the D: drive and then disconnected the H: drive, MC is currently going through your library and is fixing broken links. Eventually you will have all your music on the D: drive as you want. If you moved all your music from the H: to the D: drive, you should see the same result.
If you left both drives connected after copying everything from H: to D:, and then had MC scan both locations, then off course you will get duplicates, as you have duplicates MC can see!
What you should have done was turn off Auto-Import in MC, then copy everything from H: to D: and disconnect H:, then use the "Rename, Move & Copy Files" function for all music files, with the top drop down set to "Update database to point to new location", then with Directories and Filename unticked, tick "Find & Replace" and set "Find What" to the base music path on the H: drive, and "Replace With" to the base music path on the D: drive. i.e. If you are using the same directory path on the H: and D: drive, then you could have set "Find What" to "H:" and "Replace With" to "D:". Or you may need to include more information if you changed paths. i.e. "H:\My old directory\music" to "D:\My new directory\music".
Once that was run, you would reconfigure Auto-Import to look at the new base music directory on the D: drive, make sure that the H: drive isn't looked at any more, and turn Auto-Import back on. You could then reconnect your H: drive without MC searching it again and re-importing any files on it.
But, as you have done half the task, and it is probably still in progress, let it finish and see what happens. You may need to do nothing. Whatever you do, don't start erasing anything. That will just make things a lot worse. If MC doesn't sort itself out now, come back and ask again how to fix it.
If you do need more help, please explain if you copied or moved the files, what your settings are for Auto-Import (what directories are looked at for music), and exactly what you did when you "installed all 500 GB of your music".