The trick is to set your keyboard in Flash-Mode, means in my case, press the ESC-Key during connect over USB-A. After this the Message „Atmel DFU device connected: ATMEL ATm32U4DFU (03EB:2FF4:0000)“ appeared and the keyboard was ready to flash.
The Firmware is made with config.qmk.fm (Google Chrome required), choose your Keyboard, choose a Name for your Layout and Compile, after that „Download Firmware“. Use the hex-File in QMK.
Useful:
QMK under macOS
Keyboard-Matrixes