Hi Kris,
You will have to grab your certificates from the old installation and install them on the new machine, because the backup will not take care of custom certificates. The restoration will only generate temporary certificates just to get the system up and running.
If you want to install your custom certs, log in to the machine via SSH, and replace the existing ones with your own
Look at these paths here:
/var/lib/3cxpbx/Instance1/Bin/Cert/
/var/lib/3cxpbx/Bin/nginx/conf/Instance1/