Trying to apply SP3 update on an existing 2010 SP2 server.

Setup prompts to /preparedomain even though it has already been done.

Went back tried to run all the various forms of preparedomain (preparealldomains, prepare specific domains etc.) and the issue still persists.

Double-checked all permissions (enterprise admin, etc.) 

Any idea what the issue could be?

Try to run the  SP3 from an elevated command prompt instead and see the results

Example:
C:\Temp\SP3>setup.com /m:upgrade /InstallWindowsComponents

Also check the exchange setup logs  and see the results

Tried - I've looked at the exchangesetup logs and there are no obvious errors or complications. At the end it just states 

[09/13/2015 04:47:37.0342] [1] [REQUIRED] The local domain needs to be prepared (via 'Setup /PrepareDomain') before server roles can be installed.

Hi,

You can use this procedure to verify that Active Directory replication is functioning properly on a domain controller.

Open a Command Prompt as an administrator and type dcdiag /test:replications .

https://technet.microsoft.com/en-us/library/cc816863(v=ws.10).aspx

Then we can reprepare domain to test.

Regards,

David 

Hi,

Have you seen any error message during the prepare domain process?

Firstly, we need to check the permission to prepare the Active Directory Schema and Domain.

To prepare the schema (Setup.exe /PrepareSchema), the account used to run this cmd must be a part of the Schema Admin and Enterprise Admin group(s).

To prepare the domain (Setup.exe /PrepareAD), the account used to run this cmd must be a part of the Enterprise Admin group.

If the permission is correct, I suggest you can reprepare schema and AD to test.

Regards,

David 

All completed with no errors.