Inconsistent fileset after building ROS2

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I am cross compiling ros2 and after cross compiling all packages successfully, I create a fileset for the list of files generated in the install directory. I get inconsistent filesets each time and the files that are missing are shell scripts for setting the ros2 environment for various packages. For example those files where missing from one build and not the other:

not found: "/opt/ros/foxy/share/ament_cmake_export_definitions/hook/ld_library_path_lib.sh"
not found: "/opt/ros/foxy/share/ament_cmake_export_include_directories/hook/ld_library_path_lib.sh"
not found: "/opt/ros/foxy/share/ament_cmake_export_libraries/hook/ld_library_path_lib.sh"
not found: "/opt/ros/foxy/share/ament_cmake_export_link_flags/hook/ld_library_path_lib.sh"
not found: "/opt/ros/foxy/share/ament_cmake_include_directories/hook/ld_library_path_lib.sh"
not found: "/opt/ros/foxy/share/ament_cmake_libraries/hook/ld_library_path_lib.sh"
not found: "/opt/ros/foxy/share/ament_cmake_python/hook/ld_library_path_lib.sh"
not found: "/opt/ros/foxy/share/ament_cmake_version/hook/ld_library_path_lib.sh"
not found: "/opt/ros/foxy/share/connext_cmake_module/environment/connext.sh"
not found: "/opt/ros/foxy/share/gtest_vendor/hook/path.sh"

Please note that the missing files are random and they are never the same set, but they are always shell scripts.

I would like to understand how those scripts are generated and how to best troubleshoot this issue to make sure I have a consistent fileset generated everytime I build ROS2.

Thank you