After getting the first board rev from Sophi, I wanted to test out programming it using an FTDI programmer from Sparkfun. Couple of issues - using a new mac with USB-C hubs, the board didn't get recognized by the mac. The other problem was that the boards come wired at 5V, whereas our board was at 3.3V. I had initially mixed up these issues and thus corrupted the bootloader, this manifested in the board not being recognized anymore when trying to program.
To burn the bootloader, we used an AVR programmer and soldered some headers to the board according to these pinouts.
Connect the AVR programmer to your laptop USB port and then select these board options. The go to the bottom and select Burn Bootloader.
The board will light up. In order to program the bootloader, make sure that the headers are disconnected from the AVR programmer (even if the programmer is not connected to the laptop). Also cut the trace between the 5V and middle pad, and bridge the middle pad to the 3.3V pad with solder on the FTDI board.
Now I was able to upload the scripts again to the board and happy days!