I recently installed spybot search & destroy on Parallel and I like the immunization feature, but I'm not sure what would happen if I let it immunize my entire system, including my mac files. Would it affect my mac if the files are immunized?
The Spybot Search and Destroy app is a Windows application and will not affect your Mac files. The app will only run when you have your Windows VM loaded in Parallels. If you need to run an app to search out malware on your Mac, download the free Malwarebytes Anti-Malware app.
I would not use Spybot at all.
just a reasonably AV app in the VM. And perhaps the Antimalware Malwarebytes app. It never found anything in my VM's but it does not hurt.
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