Hi,
I did have same problem with this.
A new code file was added and this file was not visible on the SonarQube.
When i have opened \.sonarqube\out\<any number>\output-cs\file-metadata.pb file with notepad, i have seen the file which was not load to the SonarQube is encoded with windows-1252.
You can see the other files have encoded with utf-8.
After i changed this source code file encode format to utf-8 and scan the project, i could see the file and bugs on SonarQube .
Now i have a question. Is it necessary to use sonar.sourceEncoding property?
Does it work if I use it?