Hi @Rex_Andrew - welcome to the community.
I’m not clear what you mean by “SonarQube Scanner CLI version 3.0 for SonarQube MS Build”.
The Sonar Scanner CLI and the SonarScanner for .NET (formerly MSBuild) are different things.
The SonarScanner for .NET does not use a properties files. You can pass parameters to the SonarScanner for .NET in a SonarQube.Analysis.xml files as described in the docs linked to above, or you could set the inclusions/exclusions in the SonarQube UI.
If you are using inclusion/exclusions to disable the analysis of specific languages, have a look at this thread which suggests a couple of alternative approaches.