There is a 6-pin header on the Beagle Bone which you can plug this adapter cable into. The other end is USB, and then you will need a terminal program on the computer.
I use a Linux terminal emulator called screen.
When you connect in this way, you will have full access to the file system and you can fix whatever it is that got changed. This method bypasses the complex networking stuff like USB or Ethernet.
Another very practical approach is to use the Micro-sd memory cards and do not flash to the onboard flash drive.
Be sure to get a ruggedized card and it will be more reliable. I'm done with the cheap cards, they will waste your time.