Dear Nicole O'Gorman,
Good day! Thank you for posting to Microsoft Community. We are happy to help you.
As per your description, please let us cooperate and please don’t worry, we can work together to narrow down and resolve the situation.
Since you mentioned you migrate file data from Box to a SharePoint online document library site and there are no/empty files within the subfolders top-level folder.
To check if this problem related with migrate file data from Box, if possible, could you please try to copy or create a top-level folder structure including file (for test purpose) into another local location (out of Box) and then try to drag and drop the top-level folder into SharePoint online document library and verify the result with us, it will help for us to narrow down your problem.
Or Download documents from Box to local drive and upload them to SharePoint Online.
Meanwhile, you may also try below steps and verify the result with us.
1.Sync your SharePoint online document library into your File explorer and then drag and drop the top-level folder in to sync SharePoint library in a file Explorer.
2.Could you please access SharePoint online document library and click on "Upload" option and select the Folder to see if there is any difference.
3.Try to Use Microsoft Flow to copy files between Box and SharePoint.
Your understanding and patience will be highly appreciated. I hope that you are keeping safe and well!
Sincerely,
Waqas Muhammad