Apps debugged using VS Code using BLE emulator won't work as the initialization time of the COM port always takes longer than the timeout of the linking the debugger VS Code/simulator.
In 4.0.7 changelog, "End the Visual Studio Code debug session if launching app failed or sim crashed." -> This is the root of the issue. Please fix ASAP.
Please see full discussion here:
https://forums.garmin.com/developer/connect-iq/f/discussion/284513/simulator-apps-can-t-start-once-nrf52840-dongle-is-attached-on-com-port/1370662#1370662