During Public Folder Synchronization from Exchange 2013 to Exchange 2013, Mail enabled Root public folder became hidden from GAL, regardless of the source configuration. What's more, when a 2 way Synchronization is enabled, the source folders will also become Hidden from the GAL.
Incorrect processing of these settings for Root public folder.
A change request has been created, and the fix is due out for 8.14 of Migration Manager for Exchange around the end of August 2017.
A fix for the 8.13 version of Migration Manager for Exchange is due out mid September 2017.
The CR# is "MMEX3123"
To workaround the issue:
Possibility 1. Do not create root folders that are mail enabled to be synchronized by Migration Manager for Exchange. IE. Do not create a collection that goes Folder 1 (Mail Enabled) to Folder 1, instead chose the folder above it which perhaps isn't mail enabled. This will allow our tool to synchronize properly, and will not affect all subfolders which are mail enabled. The issue ONLY occurs when it's root folders that are mail enabled.
Possibility 2. Do not use the built in "Copy Mail Enable Status" of the product, where if the folders are mail enabled in source, the product can initiate the mail enablement status on the target. Instead, allow the regular folder, permissions, and data to synchronize over, but instead, mail enable the target root public folder natively / manually.
To adjust if the product is to mail enable the target folders, (On the Exchange side of Migration Manager) select Tools > Options > Advanced Agents Management > Select the option in the drop down box to "NEVER"