I don’t even remember what I did. I think I tried to use the new firmware through the new method without updating the bootloader first. My device works and I can consistently restart it and get into usb mode. But I cannot open any folders or move any files over to the device without an I/O error. Is there a way to fully wipe the device and flash firmware with the usb port or something?
I would suspect the SD card being the root cause of the problems.
The bootloader sits in the flash address space that can be touched only when updating the bootloader. If the controller is not starting up but you are able to open the bootloader it almost always means that the firmware is unable to use the SD card. The fact that you have issues with accessing the SD card from the bootloader supports that too.
If you have the controller with the SD card slot on the side, remove the card and follow the instructions at: A broken SD card | Electra One Documentation
If it did not help, it is possible to fully restore the flash image on the controller over the USB using Renesas (processor manufacturer) tools. It requires Windows or Linux computer though. I will provide instructions if needed. Pls start with the SD card first.