We do test toolchain updates with VisualGDB and it should normally work out-of-the-box. Most strange errors like this one happen when trying to apply several changes at the same time and ignoring various error messages, or by modifying the project structure directly, hardcoding the paths that should be normally referenced via variables.
If you often modify the projects manually, please make sure you read this page first. It explains the embedded project structure in detail.
That said, if you can confirm that installing a specific update consistently breaks some functionality, and provide repro steps for us to reproduce the problem on our side, we should be able to fix it.