I know this is an old post, but I figured I'd add this information as I ran into it.
I don't think it is related to autogen or timestamps, I believe it is related to precompiled header files in general, because some of the failures I ran into had nothing to do with autogen, even thought some of them did:
/Fdqtbase\src\openglwidgets\CMakeFiles\OpenGLWidgets.dir\ /FS -c qtbase\src\openglwidgets\CMakeFiles\OpenGLWidgets.dir\cmake_pch.cxx Microsoft (R) C/C++ Optimizing Compiler Version 19.29.30153 for x64 Copyright (C) Microsoft Corporation. All rights reserved. ninja: build stopped: subcommand failed.
11:55:53 [836/4092] Building CXX object qtlanguageserver\src\jsonrpc\CMakeFiles\JsonRpcPrivate.dir\cmake_pch.cxx.obj 11:55:53 [837/4092] Building CXX object qtgrpc\src\protobuf\CMakeFiles\Protobuf.dir\cmake_pch.cxx.obj 11:55:53 [838/4092] Building CXX object qtserialport\src\serialport\CMakeFiles\SerialPort.dir\cmake_pch.cxx.obj 11:55:53 [839/4092] Building CXX object qtconnectivity\src\nfc\CMakeFiles\Nfc.dir\cmake_pch.cxx.obj 11:55:53 ninja: build stopped: subcommand failed.
I was able to work-around it by disabling precompiled headers files by adding -DCMAKE_DISABLE_PRECOMPILE_HEADERS=ON to the CMake generation step. I was using the CMake with Visual Studio 2019 ( 3.20.21032501-MSVC_2) on Qt 6.7.3.