Hi,
VisualGDB should normally already use the relative paths as reported by CMake. However, if your codebase spans across multiple drive letters or some CMake files use absolute paths to refer to the source files, the absolute paths may indeed end up in the VisualGDB’s settings files.
If you can reproduce the problem on a clean project and share the steps we could follow on our side to get the same behavior, we will gladly look into it and try to suggest a workaround.