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What you have witnessed is the CompactLogix reaction to a failure of the 1769 bus. This is a protective feature of the controller that clears the user program and shuts down the I/O.
I very strongly recommend using the ordinary memory clearing mechanism of the CompactLogix:
1. Disconnect power from the CompactLogix power supply.
2. Remove the CompactFlash memory card from the CPU, if present.
3. The battery is on the left side of the CPU, under the plastic cover. Disconnect the battery connector and wait ten seconds. There is no "short two pins" or other process required.
This is a totally ordinary, completely normal, as-designed way to clear the user memory of a CompactLogix controller.
The EtherNet/IP port configuration is not stored in user memory and will be retained. You can reconfigure it with any of the ordinary methods: use RSLinx through the serial port, or use the BOOTP/DHCP Utility.