In WHM, there is a tool called DNS Cleanup. This tool will clean up the nameserver configuration file and remove any duplicate entries.
1) You can find it under DNS Functions.

2) Click Perform a DNS Cleanup.

3) Heed the warning and make sure you aren't editing any nameserver configuration files during the cleanup.

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4) Proceed when ready.
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That's all there is to it! DNS Cleanup complete.

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This is the end of the tutorial. You now know how to perform a DNS cleanup in WHM.