Thank you @prototypicalpro for your help.
Unfortunately upgrading the bootloader to V2.0.0 didn’t solve the problem on my board.
The program stops at the normal initial breakpoint at init(); After hitting F5 my PC shows the Message box with ‘USB device not recognized’ at the lower right corner of the screen and debugging is not possible.
(This is different to the behavior with the other bootloader where had 'received signal SIGTRAP and the program stopped in the micros() routine). I If I click the ‘Restart’ button (CTRL+SHIFT+F5) after reaching the initial breakpoint at init() and then hit F5 after it stops again at this initial breakpoint I can bebug as expected.
If I add ‘debug_init_break =’ to my platformio.ini as suggested by @mauelbl the program stops at ‘void Reset_Handler(void){’ (see picture above) and my PC gives the same ‘USB device not recognized’ message.