It seems like the Make a Copy option only works for individual files (not for folders).
When somebody shares a folder with me on Google Drive, how can I make a copy of that folder in my own Google Drive account?
A Google Drive migration extension is available in Chrome extensions store, you can copy the entire folder with that.
Download extension from here. https://chrome.google.com/webstore/detail/drive-migrator/nakklajdcijlkfagghhcdofbgbhddoed?hl=en
Step1 : Install extension in chrome browser.
Step2 : Open your Google drive account (primary) where all your file exists.
Step3 : Share that particular holder to your secondary Gmail account.
Step4 : Open your secondary Gmail account, select the shared folder and copy all the files with the extension.
Step5 : Now go to Primary account folder and delete.
I just had exactly the same issue. And I copied everything successfully via this open-source service: https://github.com/ericyd/gdrive-copy
After you finish your copy, do remember to revoke your granted permission to this app.
Here's another way to copy a folder with an external application:
*The service is free up to 50 gigabytes per month.