Hi,
I have found that the qstlink2 (v1.2.3) fails to upload binaries if the STLink2-1 version is 2.28.16. I've noticed that there is a closed ticket already and I did use the ppa to install the 1.2.3 but I believe the issue is still there. qstlink2 works fine (with the same binary file) if STLink2-1 version is 2.23.9.
Also the STM32-Utility uploads the binary file with no problem if the STLink2-1 version is 2.28.16.
I was able to mitigate the issue by downgrading STLink2-1 to 2.23.9.
For future sake, I've attached my binary (blinky) for STM32F429ZI-Nucleo.
Dummy_Blinky.zip