Hi,
The Android NDK build system usually expects all the source files to be in the jni subdirectory of the project. VisualGDB updates the LOCAL_SRC_FILES list automatically on each build based on the files that are part of the project in VS. You can disable this behavior by removing the comment line above the variable.
The simplest way to use your existing source in the new app would be to copy the sources to the jni directory and then adding them as existing items to the project in Visual Studio.
You can also try to use the existing sources from their current location (disable the VisualGDB source files updating then). The source files should be added with their relative paths to LOCAL_SRC_FILES and the relative include directories to LOCAL_C_INCLUDES in Android.mk. Please read the ANDROID-MK.html documentation from the docs subdirectory of your Android NDK install directory for further information on these variables.