Turns out Removing, or Rebuilding instant clone pools leaves stale dns records since the Linux DHCP Client on the Instant Clones doesn't get ran when either Rebuilding or Removing Instant Clones.

This is broken down into four steps:

-Create service account/assign service account to DHCP server.

-DHCP server configuration to allow Linux / Windows DHCP clients to work with the DHCP server.

-DHCP Lease times (to clean up orphaned dhcp leases)

-DNS Scavenging (to clean up orphaned DNS records)

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To mitigate against stale records do the following:

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FIRST SNAPSHOT OR BACKUP THE DHCP SERVER and DNS SERVER in case of any issues!

(Create a Service Account to handle DHCP/DNS records)

1. Create a service account in active directory called "dns_svc".

2. Right click on the new account, go to properties, then go to members tab , Add the "dns_svc" account to the "DNSProxyUpdate" Active Directory group. Remove any other AD groups such as "Domain Users". 

3. Go to the DHCP server in Windows Server, and click on the DHCP button to drop down the carrot, on the first level you'll see "IPv4" with a server icon, right click, go to properties, go to the advanced tab, hit the Credentials button for "DNS dynamic update registration credentials", enter in the account name using the service account we created in step one "dns_svc".

(The first three steps allow the dns_svc to handle any dhcp requests instead of the DHCP server. This is a good thing if you want to scavenge dns records later on, or if you lose your dhcp server and the records become orphaned.)

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( Configure DHCP to allow dhcp clients to handle dns records/dhcp requests )

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4. Configure the DHCP server to allow DHCP clients to manage their on DNS records, NOT the DHCP server.

On the DHCP server go to the scope that your instant clones are assigned to, right click on the scope, properties, go to the DNS tab, check the box for the following:

-Enable DNS dynamic updates according to the settings below (CHECKED)

-Dynamically update DNS records only if requested by the DHCP (CHECKED)

-Discard A and PTR records when lease is deleted (CHECKED)

-Dynamically update DNS records for DHCP clients that do not request updates (for example, clients running Windows NT 4.0) (CHECKED)

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( DHCP Lease times)

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5. On the DHCP server go to the scope that your instant clones are assigned to, right click on the scope, go to the General tab, set Lease duration for DHCP clients to a few hours, I recommend 4 to 12 hours. This step will help clean up duplicate dhcp records if someone removes or rebuilds a pool without a graceful shutdown that would normally allow the dhcp client to remove the dhcp lease record and dns record.

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DNS scavenge configuration, this will clean up stale/orphaned DNS records that have been left behind.

====DANGER, SCAVENGING RECORDS MAY REMOVE DNS RECORDS THAT YOU WANT TO KEEP=======

==TAKE A SNAP SHOT OR BACKUP BEFORE MOVING FORWARD===========

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6. Go to wherever your DNS record are stored on Windows server and right click on the DNS server icon (looks like a computer), click on "Set Aging/Scavenging for All Zones" .

7. No refresh interval, set to 1 hour.

8. Refresh interval, set to 1 hour.

9. Pop up windows appears: check "Apply these settings to the exsisting Active Directory integrated zones" (this will push changes to other DNS servers.

7. Check the box for "Scavenge stale resource records" (CHECKED)

This website helped me : Dynamic registration of DNS for Linux devices in an Active Directory environment with Dynamic registration of DNS for Linux devices in an Active Directory environment with Windows DNS se...