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Dear Justin,
Thank you for posting in Microsoft Community.
I understand that you have an issue on cannot sync shared folder from different organization.
You mentioned that your UPN has been added as B2B guess account in their Azure Active Directory.
Kindly share with us the information below:
May I know if you accepted the invitation?
What account sign on in your OneDrive sync application?
Suggestions:
Possible reason is that it is caching the other account that is why you cannot sync it.
Kindly open the link of shared folder on in-private browsing or incognito mode. Sign in your Work account/UPN from your organization, the one added as guess account in AAD.
Once sign in and you can access the folder, click on sync button, OneDrive popup then click on Microsoft OneDrive application.
Kindly double check your OneDrive if your work account/UPN is log in. Open OneDrive settings > Account tab.
Hope the suggestion can help you.
We look forward to your response. Thanks for your cooperation. Stay safe and healthy always.
Sincerely,
Zee | Microsoft Community Moderator