If you do power your board from USB, you can't just power up the power supply and have the drivers work correctly. You have to ensure that Marlin knows that the power supply has come online so it can reinitialize the drivers. The normal way to do this is by using the PS_ON pin and enabling PSU_CONTROL in the Marlin configuration. Then you can turn on the power supply with M80 and Marlin will reinitialize your TMC drivers.
Otherwise you will have to manually run M501 after turning on 12V power so that the drivers get the right initialization.
Otherwise you will have to manually run M501 after turning on 12V power so that the drivers get the right initialization.