Different Boot than Specified one

With the recent upgrades in PIO Core, the sodaq_autonomo upload stopped working for me

Just wondering does anybody know how I can list the parms that PIO sends to sam-ba and modify them.

I’m using an sodaq_autonomo SAMD21 with sam-ba upload.
board = sodaq_autonomo
platform = atmelsam
framework = arduino
upload_port = COM6

which on PIO upload, with Autonomo in boot

Checking size .pio\build\sodaq_autonomo\firmware.elf
Memory Usage → Redirecting...
DATA: [=== ] 27.4% (used 8964 bytes from 32768 bytes)
PROGRAM: [==== ] 39.7% (used 104000 bytes from 262144 bytes)
Configuring upload protocol…
CURRENT: upload_protocol = sam-ba
Looking for upload port…
Use manually specified: COM6 ;Auton#1 boot
Forcing reset using 1200bps open/close on port COM6 ;Auton#1 boot
Waiting for the new upload port…
Error: Couldn’t find a board on the selected port. Check that you have the correct port selected. If it is correct, try pressing the board’s reset button after initiating the upload.
*** [upload] Explicit exit, status 1

I realized that I had switched to the open source Adafruit Feather boot (built my own version) and programmed it into my Autonomo which had worked OK before and now has stopped working after the PIO upgrade.

I also have Adafruit Feather M0 which I plan to use in the longer term with custom daughter shield (Autonmom has Xbee socket on it).

For the Autonomo boot, I did find a workaround, when PIO starts the downloading to the Autonomo “Waiting for the new upload port…”
do the double reset again on Autonomo which PIO picks up on and downloads successfully.