I played around with certificates for separate subsites to servers on a Virtualmin box *cough*not production of course*cough* and got faced with :10000 no longer being accessible post removing a disabled site.
Failed to open SSL key /home/disabledsite/ssl.key at /user/libexec/webmin/miniserv.pl line 4405.

Scenario

I had a top level site set up, contoso.com, with a Let’s Encrypt up and running.
This top level site was disabled for one reason or another.
A new site, subsite.contoso.com got set up and developed, once ready to apply the Let’s Encrypt the wizard prompted me to manage the certificate over at the contoso.com settings, however, with that site disabled, the configuration did not take.
Solution? Remove the contoso.com site, yes?, well turns out, no, that caused the error.

Solution

Access the host via SSH,
Comment out the lines related to the borked server in /etc/webmin/miniserv.conf.
Start the service again.

sudo nano /etc/webmin/miniserv.conf
#ipcert_subsite.contoso.com,*.subsite.contoso.com=/home/contoso/ssl.cert
#ipkey_subsite.contoso.com,*.subsite.contoso.com=/home/contoso/ssl.key
sudo service webmin start