Hi there,
Awesome, Sample my Guy 
I’m waiting on some external Antenna’s to arrive for a range test. I would agree, There is something off on the West Flashing tech.
Users YMMV, The JLink is Rock Solid the more I use it the more I like the Whole package, RTT Viewer and SDK and DEV board.
I too switched to the JLink runner and haven’t had one go south yet. WIth the West Flash Tech , seemed like every 3rd or 4th flash the part would FAULT and JLink fixed them every time. I had the same as you outcomes with the (restore Script) just did NOT work reliably.
I think it’s a speed issue with the Samd11 front end.
and or the config file may need some additional fine tuning.
The 54 is a nice MCU though and I think with the MCUBoot and the DFU capabilities will serve users well who need that. More maturity on the SDK will only get better so I’M confident the Juice will be worth the Squeeze 
the Deep_throat 
is whispering a 54LM20 Xiao could be in the works with built in High speed USB and High Speed SPI, 2 Meg NVM and 512k RAM so that will be a catapult to Anything already built or understood. This is I see the advantage, You can just build for a different targets and the APP can be coded to be MCU agnostic and expandable Ram memory and Flash gives instant boost and features like crashproof DFU. Newer Soft devices are expected also for the 54 Series. Supporting some Advanced BLE features.
More RAW HorsePower(2x) @Less than (half) current consumption, Battery Status readable, BLE 6.0 with Channel Sounding. Definitely going in the right direction.
Keep them coming. 
GL 
PJ 