Hi @Barry Briggs ,
Welcome to Microsoft Q&A!
The Clean will remove all intermediate and output files created by the build process, such as .obj files.
If the source folder is removed, please check if you add a custom target to your .csproj file and it will lead to clean all contents of your folder.
In addition, you can also try to disable some third-party extensions from Extensions > Manage Extensions > Installed > select and Disable, then, relaunch your Visual Studio to check if it persists.
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