Q: No Crank, No Start After Clearing Check Engine / Security Codes?

2002 BUICK REGAL GS Supercharged: Solid Security light and solid Check Engine Light lit for over a year with the engine running fine before scanning. I scanned all systems with Blue Driver OBD2 Diagnostic Scan Tool while the engine was running. Scan revealed confirmed codes P0102 and B2958. It also displayed historical Security codes B2960, B2957 and B2961. I selected "Clear All Codes" and then the engine died. I attempted to restart the vehicle but the vehicle only clicked, no crank, no start. I attempted the GM Passlock relearn procedure but it did not work. No crank, no start and the solid Security light, Check Engine light still remain. I scanned the system again and current Security code B2958 and historical Security code B2960 are the only codes that remain. Battery is fully charged. Can a scan tool really cause a vehicle not to start? How do I fix this?

My car has 200000 miles.
My car has an automatic transmission.