Hi,
Are you sure that you’re having and running the latest Virtualmin 6.17-3 installed?
I really cannot reproduce and witness DNSSEC keys being changing on saving virtual-server.name - Server Configuration ⇾ DNS Options page. It shouldn’t be happening unless you intentionally toggle DNSSEC signature enabled option.
Perhaps, the workaround would be is to disable DNS domain enabled feature on virtual-server.name - Edit Virtual Server page and then re-enable it. Be careful, it will reset domain’s DNS zone record to default.
Afterwards try enabling DNSSEC signature enabled option and later checking if the issue is still happening?