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Dear Sam,
Thank you for posting back and clarifying the situation.
It seems that you want to know why the returning employee whose access was removed when they left still have access to previous resources in SharePoint Online site.
It may because that the returning employee's access to previous resource has not been completely removed.
If you still want to remove his access, may I know if you have tried using following PowerShell commands?
Remove-SPOUser -Site https://fabrikam.sharepoint.com -LoginName ******@fabrikam.com
*Note: Replace the *****@fabrikam.com placeholder with the returning employee.
For reference: Using the SharePoint Online Management Shell
If my understanding of the scenario is not consistent with yours, feel free to point it out, I will continue helping you.
Thanks for your time and cooperation! Hope you have a nice day.
Sincerely,
Tina | Microsoft Community Moderator