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If you have a registrar module enabled, the nameservers are returned by the registrar via API. If you are a registrar, then your nameservers would likely be returning this information via query from your WHMCS. Im sure there is some module or integration for storing these values on your local WHMCS, but as far as I know WHMCS always attempts to retrieve real-time nameserver records from the registrar.

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You should also verify the settings in Setup -> General Settings -> Mail

A server module that supports VPS provisioning, like solusvm or virtualizor can help you accomplish your goals!

Depends on what you're aiming for, but you could just import a fresh tbldomainpricing to your DB to mass import TLDs and pricing configurations. But if you're planning to use a registrar module with your WHMCS, you might ask your registrar whether they have any WHMCS addon modules for TLDs, as there are several. Typically, these also have some bulk pricing management functions as well, which can save additional steps.

What server module are you using? Typically, the server setup process will have some level of custom instructions that explain the process.

This sounds like a great addition to the module

I would like to apologize for my earlier post referencing the module logs. I believe domain synchronization is logged seperately and the logs can be configured as email reports sent to admin users. The receiving admin emails should have access to this feature, which are configured in WHMCS User Management in Admin area.

Perhaps, we need more information regarding your planned implementation of multiple domain names for your WHMCS. How will you keep your license from reporting errors? I'm sure that it can be done, but I'm also sure there are ways not to do it, and this is what you'd need to have figured out prior to any customization.

Some registrars do not support Domain Sync and some may have custom sync scripts. Double check that the registrar module supports sync, then if so, check the logs for more details. WHMCS Admin - > Utilities -> Logs -> Module Logs

It's not turnkey, but it's as close as it comes with prepackaged modules. Let me know how it goes.

BusyRack also built DNS management module that connects to cPanel DNS clusters. It can be configured to bypass the registrar DNS management in favor of hosting/managing the DNS from these nameservers.

It is not mandatory to use Auto Release module. To my knowledge, the existence of Auto Release server module will not affect existing server modules. You should not use Auto Release module if it is causing interruption of your desired/expected workflow.

This could be tricky as WHMCS requires a template declared in tblconfiguration which will cause one template to be cached in favor of others. I think there are some third-party workarounds available, however, that might be helpful, specifically ModulesGarden has one that supports multiple stores in one and supports multiple templates.

Enable the error logging and verify the tblconfiguration values, in addition to verifying that your CDN is configured appropriately.