Remove orphaned AD group permissions from migrated Sharepoint site

I used the Sharepoint Migration Tool to move user home directories to OneDrive, but I didn't realize it was going to copy over the ACL from the fileserver. Now my user's OneDrive Documents libraries have orphan permissions entries from on-premise groups like this:

Display Name        Login Name                           Groups
------------        ----------                           ------
HelpDesk            c9678887-a0e9-4975-9b06-c07d1204620d {}
All Users (windows) windows                              {}
Everyone            true                                 {}
Department Group    219b3351-0287-4f2e-8586-8dcd730d0552 {}
Everyone except ... spo-grid-all-users/9fd7580a-6472-... {}
Server Admins       6ea88195-b9c5-47c0-8161-ef24e2182b50 {}
SharePoint App      app@sharepoint                       {}
_spocrawler_27_3549 ylo001\_spocrawler_27_3549           {}
System Account      SHAREPOINT\system                    {}

Remove-SPOUser returned this error:

PS C:\Users\jay.carper> Remove-SPOUser -Site $url -LoginName "c9678887-a0e9-4975-9b06-c07d1204620d"Remove-SPOUser : Cannot complete this action.
Please try again.
At line:1 char:1+ Remove-SPOUser -Site $url -LoginName "c9678887-a0e9-4975-9b06-c07d120 ...+ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+ CategoryInfo          : NotSpecified: (:) [Remove-SPOUser], ServerException+ FullyQualifiedErrorId : Microsoft.SharePoint.Client.ServerException,Microsoft.Online.SharePoint.PowerShell.
   RemoveSPOUser

Does anyone know how to remove these orphaned permission entries? I don't think they hurt anything, but it would make everyone in the organization feel better if I could remove them.

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