Thanks Bruce
I appreciate the information and it helps me understand a bit more of what could be happening.
Currently my QNAP NAS is defaulting to self signed certificates because I cannot get any Lets Encrypt ones installed.
To build on my problem explanation:
I recently implemented a new mail server on this machine and used lets encrypt for the domain mail.kerrzone.com.
On this same NAS I am running an apache http server (the QNAP default) with port 80 and 443 open and I had successfully installed a certificate for tenyearsafter.myqnapcloud.com including alternate sites kerrzone.com and musings.kerrzone.com.
After three months the mail server renewed automatically, no issues but when the web servers certificate auto renewed it dropped the alternate sites.
Unfortunately QNAP control panel interface for certificate management does not have an option to use the test environment. (The mail server does and I used test first no problem).
I tried adding the alternate sites back from control panel using kerrzone.com as the main domain with musings.kerrzone.com and tenyearsafter.myqnapcloud.com as alternates and received the error :A domain validation challenge was not received from the acme server. Ensure your router and QNAP device both accept inbound traffic on ports 80 and 443 which is a requirement from let's encrypt.
I have used a couple of online apps to confirm these ports are open.
I used the QNAP interface at my QNAP cloud to release the single tenyearsafter.myqnapcloud.com interface and then tried the control panel app to add it back with the alternative sites using kerrzone.com as main domain. It did not work still with the authentication issue.
I did then try both the control panel interface and the myqnapcloud interface to add the certificate using tenyearsafter.myqnapcloud.com as the main domain. I guess I tried this too many times and this gives the rate limit issue for this domain.
I wonder if the issue getting the alternate domains is related to the mail server certificate, although not sure how and it did work initially.
I am going to try moving the mail server to a different host machine and try and certify there. If this works, After March 28th I will try and add the qnap only cert to the tenyearsafter machine.
If you or anyone else on the forum have any thoughts about this considering the additional information please let know.