This is a warning/note, maybe a question if any one else is having this issue.
Uploading to the MKR1500 - the bossac command from the IDE (.arduino/packages/bossac-1.7.1-arduino3) - works fine.
However - when you use the standard bossac (1.9.1 is current), it breaks everything.
Be wary - you can just copy the bossac from arduino and use that. If you use the current version of bossac, then no matter what the command, it will break your bootloader and you need a second SAMD board to recover.
If any one has had bossac working consistently plz lmk.
Have you tried it with the version 1.9.1-arduino2 that Arduino distributes?
Arduino maintains a modified variant of bossac, which is what is installed and used by the official boards platforms (and likely also by many 3rd party boards platforms, but the platform developer can specify any arbitrary tool dependencies, so some might also use the mainline bossac). The source code for Arduino's variant is hosted here:
You can see the modifications made by Arduino in the commit history of that repository. This one looks possibly relevant:
If the fault also occurs with 1.9.1-arduino2, this would indicate that the different behavior is probably caused by some change in the mainline bossac between 1.7.1 and 1.9.1. If the fault does not occur with 1.9.1-arduino2, this would indicate that the different behavior is the result of the differences between Arduino's variant and the mainline bossac.