Hi ,
The root hints can be removed permanently and completely by removing the root hints from the DNS Manager, the CACHE.DNS file and from Active Directory.
The root hints come back is because the root hints still exist in the other two locations (CACHE.DNS file and Active Directory). And you only removed default roothints entries from the cache.dns file.
For more details, you could refer to the following link:
https://support.microsoft.com/en-us/help/818020/root-hints-reappear-after-they-are-removed
Please Note: Since the web site is not hosted by Microsoft, the link may change without notice. Microsoft does not guarantee the accuracy of this information.
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Best Regards,
Candy