It's very common for the EEPROM to become corrupted if you are frequently downloading and testing new firmware. The recovery process on the SDK will be the same as if you were recovering a WICED Sense Kit. However, if your custom board didn't take into account the recovery process you may need to flywire off your board. See the link that boontiongt_56 attached above for more detailed instructions. The goal is to power cycle with SDA pulled to ground. And afterward, release the ground from SDA. THEN proceed with the SDK recovery process.
It's concerning that the second COM port disappeared. They should appear no matter the state of the Broadcom chip on the other side (unless there is a short). I recommend trying an alternate programming cable.
I got sorted in the end.
I had had to use the bcm920737tag to recovery my custom board. Had to turn off all the dip switches expect 5v and 1.8v. I had the bring the voltage of my custom board down to that of the bcm20737tag (1.8v)
i had had to jump the tx of my custom board to the tx off the tag, same for rx and a common ground.
i them pulled my Sda high and released it using a jumper wire.
This got me out of a hole. But long tern it time consuming.