Seems like a janky feature of NRF SDK for VSCode may lead people to blow away the bootloader. If you click anywhere on or to the right side of the “chip” icon, you will erase all and flash. Otherwise, it will flash. Photo here nRF Connect for VSCode Flash command erase all flash(es), need to erase only "app" sector. - Nordic Q&A - Nordic DevZone - Nordic DevZone
Confirmed, I can get shell_nus flashed and functional via the vscode based project. I will update this issue when I have a configuration that looks reasonable.