When your launch your IDE and it has over 40 updates and one of them randomly fixes the reason your development board was not working you have a problem. The idea of the development board is to have a known environment, not in this case, it could be broken or it could be that the IDE wants an update.....
ah you unlocked some memories. At the time i was evaluating the ATSAMC21 using the xplained board under atmel studio (couple of years before they were bought by microchip) and that's exactly what happened from time to time
Atmel had this "smart" (to me idiotic) feature of things being automatically recognized as connected then unlocking some menus and features and examples, whereas for microchip (or ST or NXP for that matter) you select the processor and only then you can select the available dev boards. period. And it will check if it's connected only when the IDE needs it and it care it will ask what to do.
Silabs does the same shit as atmel do, but at least it works. Their radio configuration app hasn't received an update in i don't know, 5 years?
I wonder if newer devboards for atmel parts that use the PK4OB have the same "features" or they dropped that and you have to manually select things like in microchip devboards
I'm really sorry i can't be of any help because in the end i don't use atmel parts, all that pile of issues is unknown to me
I wonder, can you not use the debugger on board and use an external debugger instead?
Edit: re-reading apparently you have issues with packs? can't you select an older pack version, os use an older compiler version?