It's quite easy to create duplicate folders in Google Drive.
Let's say you have a folder called January in a 2016 folder and a folder January in a 2017 folder. If you move the first January folder into 2017 you'll get a duplicated folder. Unfortunately, Drive not only does not merge the folders as you would expect; it doesn't even warn you of the duplication.
Here's a simple tool that scans your drive for duplicated folders, (folders with the same name in the same parent folder), and merges them if you wish so.
This is a client side tool, keep the page open until the merge completes. Your Google Drive data and credentials are never sent to a 3rd party server. You should create your own Oauth credentials as explained here: https://developers.google.com/drive/v3/web/quickstart/js
This tool is a proof of concept, use it at your own risk.