Today I have been migrating Public Folders (yuk!) from Exchange 2010 to Exchange Online, and have come across a slightly odd issue.
I had followed the lovely guide to Public Folder migrations provided by Microsoft here, however I could not complete my migration as the migration batch had completed with errors. The error I was receiving was as follows:
Error: MigrationMRSPermanentException: Error: There are 2 mail public folder(s) in Active Directory that were not linked to any public folder during migration.
The Public Folders referenced in the error message were both Exchange system folders, so I wasn’t sure why it was bothering to try and synchronise them. Luckily the error message does give us a clue as to what to do;
You may also run "Set-MailPublicFolder -IgnoreMissingFolderLink:$true" for each AD object that is a legacy system folder and resume the migration
Being the silly person I am, I assumed that this command needed to be run against the legacy Public Folders On Premise, but apparently -IgnoreMissingFolderLink is not a parameter in Exchange 2010. What I actually needed to do, which is not obvious from the error message, was to run this command in Exchange Online. I ended up using a catch all command, which looked like this:
Get-MailPublicFolder | Set-MailPublicFolder -IgnoreMissingFolderLink:$true
Once this was done, I stopped the migration batch, and then started it again. It then performed it’s initial sync and I was able to continue the migration!
Miss Tech 
Just came across your article and I have a similar problem.
In my case, some of the folders are production ones.
Q/
When Public Folders are onboarded to Exchange Online do they have to be mail enabled?
Q/
If I use the command “Get-MailPublicFolder | Set-MailPublicFolder -IgnoreMissingFolderLink:$true” will all the content belonging to the affected Public Folders be copied over anyway but just not mail enabled?
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I swear to God, public folder migration to Office 365 has been the bain of my life for the past few months.
So many issues trying to get this working. At every hurdle there seems to be errors.
I’ve finally got to a stage where I have created a migration batch and its syncing. Except it error’s out on one of four mailboxes with the error above.
Even speaking to Microsoft they have failed to mentioned the, what now seems simple direction.
I have to wait 26 hours for that mailbox to sync where it will either work or display another error message.
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I have a public folder migration but different error, appreciate if you can help me out. I’m migrating from exchange 2013 to Office 365 and got this error:
Error: MigrationMRSPermanentException: Error: There are 2 public folders that could not be mail-enabled.
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Thanks Emily! Trying this solution.
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Thank you very much 🙂 Really helpful
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Thanks Miss Tech…I’ve been meaning to thank you properly for, literally, a few months now, and finally remembered to do so today. Back in July I was doing a cutover migration from Exchange 2013 to Exchange Online (Office 365), and hit the same problem you describe above with my public folder migration. Microsoft Support wasn’t much help; in fact, they gave me bad advice for this part. If I hadn’t found your article, I don’t know if I’d have made my deadline. So, thanks for saving my butt! Much appreciated.
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