Check the folder permissions. If I understand correctly, the DFSRoots folder is empty when you access it locally on the namespace server (DFS root server). However, the folders (links) are visible if you access the namespace by using DFS share path, such as \\domain.com\dfsroot.
Please help check the following:
1. Do all namespace server encounter the issue?
2. Do the DFS objects exist in AD domain partition? You can verify it by using adsiedit.msc, then navigate to Default naming context\CN=System\CN=Dfs-Configuration
3. Does AD replication work properly in the domain?
Thanks. I hope it will help you.
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