Okay I believe I found the solution.
For those in the future that may come across this problem:
1. Pull the plug. Shutting down is not enough, physically pull the plug from the power supply. (It appears something was saved on the hardware that prevented the eth ports from resetting to their previous state.)
2. Create a backup of your flash drive, and replaced the network.cfg and network-rules.cfg (Luckly I had a backup of these two files to use. Also make sure to use the same exact flash drive. Do not use another drive with your backup files as this caused the boot to hang.)