I managed to program the bootloader back to the board with an Atmel-Ice. It works fine now!
The problem was that I was experimenting with command line uploader (bossac), and accidentally erased the full flash.
By the way, I noticed that the bootloader I was using before this incident, was probably outdated!
I couldn't upload any program to the board that was greater than 124KB (~50% of flash memory of Sodaq Sara). At the end of the upload process I got an error message saying
and the upload was never completed.
After programming the new bootloader back to my board, this issue is gone! Now I'm able to use the whole flash memory capacity, so I quickly refreshed the bootloader on the other boards too