There are no viruses attacking your LE certificates.
If you suspect you have an infected application and you want to delete the app then go ahead and delete it.
You don't need to delete site routes, domains, certificates, or anything else.
We haven't settled on a packaged virus scanning solution here yet but we're pretty good at spotting them manually. If you're concerned about malware or whatever then please contact support with the details so that we can look into it.
