I am working with a very big project (a solution that contains 16 projects and each project contains about 100 files).
It is written in C++/C# with Visual Studio 2005.
For C++ resources, did you try right-clicking the project in "Resource View" and then deleting the ones which do not have a tick mark next to them? It is unsafe to delete unused dialog resources since they are referenced as "enum"s in code (like the following).
enum { IDD = IDD_ABOUTBOX };
..however for all the others it should be safe.