@MartinL , thanks to you I have advanced a step, on a fresh computer, the board is recognized as a Arduino Zero after uploading your bootloader. After replacing the bossac.exe with your file, I was also able to program the board (I selected Arduino Zero - Native USB Port) and I got the following message:
Atmel SMART device 0x10010094 found
Device : ATSAMD21E17D
Chip ID : 10010094
Version : v2.0 [Arduino:XYZP] Oct 2 2021 13:30:30
Address : 8192
Pages : 1920
Page Size : 64 bytes
Total Size : 120KB
Planes : 1
Lock Regions : 16
Locked : none
Security : false
Boot Flash : true
BOD : true
BOR : true
Arduino : FAST_CHIP_ERASE
Arduino : FAST_MULTI_PAGE_WRITE
Arduino : CAN_CHECKSUM_MEMORY_BUFFER
Erase flash
done in 0.444 secondsWrite 11440 bytes to flash (179 pages)
[==============================] 100% (179/179 pages)
done in 0.072 secondsVerify 11440 bytes of flash with checksum.
Verify successful
done in 0.011 seconds
CPU reset.
However, the board disappears after that and the port sub-menu in Arduino is grayed out. The board is recognized again after double tapping the reset button, but my code does not seem to run. It is the simple Blink code that should turn A4 (which is pin PA05, i.e. pin number 6 of ATSAMD21E17D chip) on and off. But the pin seems to be floating and does not oscillate. Any suggestions?