After disconnecting/reconnecting all 12 zone wires to locate valves, your Toro EL-12+ now runs only the first non-OFF zone regardless of selection. This suggests a common wire wiring error or controller damage during the process.
The Toro EL series uses a dual-common system: one common for "lawn" zones, one for "shrub" zones. If you swapped the two common wires (or combined them incorrectly), the controller's multiplexing logic gets confused—exactly the symptom you describe.
The controller's multiplexer/driver IC may have been damaged by a static discharge or momentary short during wire handling. The EL series is sensitive. Options:
Document your wire-to-terminal mapping with photos before any future work.
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