It must be a big headache of you, doesn't it?
Take it easy, there is always a way to solve it.
And I would suggest you to use a wonderful software to fix it.
Besides, no matter you want to fix music tags, fill up missing covers, remove missing tracks or delete duplicated songs, you can finished these tasks with this program.
So you should download and launch it on your windows, then choose "Manage" and you will see the "Organize", click on it and tap on the "Scan" icon later.
Then wait for the result of the scanning, and you will click on the green "Fix" button to fix the duplicated tracks when the scan process is done.
And all the duplicate songs will be clean up.