Thanks for sharing your project, I have checked on my side (I enabled the BLE without any change because in the ioc shared its activation was missed), I did not reproduce the issue and the hw.h file is well generated in the project under \Middlewares\ST\STM32_WPAN\interface\patterns\ble_thread, could you please check with the Latest CubeMX (6.2.0) and CubeIDE version?
A complex system that works is invariably found to have evolved from a simple system that worked.A complex system designed from scratch never works and cannot be patched up to make it work.