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Hi I Wanna License,
I understand you want to migrate one subfolder from a folder to another folder in the SkyDrive Pro library on SharePoint Online.
If you want to move one single file to another folder directly on SharePoint Online, you can select this file and click Send To:
Then fill in the address of another folder. (The address can be seen in the folder property)
Moreover, using SkyDrive Pro 2013 client sync can easily meet your requirements when moving multiple files. You can use it to sync files and folders between the SkyDrive Pro library and your local desktop. After doing it, you can manage the folders in this SkyDriver Pro library just like managing local files in the windows explorer. “Copy”,”Paste”, and “Delete” are available for the folders and files, and you can also drag and drop them based on your needs. Here is an article to help you sync the library to local desktop: Sync a library to your computer.
Are there any updates? Is there more assistance needed here?