Please be sure not to re-arrange the folder structure in your destination Drive account while the restore is in progress. Restores for Google Drive have 3 phases.
1. We restore all folders to the target account
2. We restore all files into the target account on a single level
3. Once all files are restored, we place the records into their proper folders and build the proper hierarchy.
Be aware that editing folder structure in the target account before the restore is complete can interfere with the third phase of the process and may result in some of your folders not being arranged into the proper hierarchy. It is a best practice to not alter folder structure in the target account at all until the restore has completed.