The LEDs at the 4 and 5 PM positions (not shadows at 4 and 5, but LEDs) are D106 and D610– again both connected to the LED6 line.
It sounds like you may no longer have a connection between the microcontroller’s output and that control line LED6. If you have a multimeter, you might be able to locate the issue that way. But in any case, try to look and see if you can identify any damage (broken/scratched wire trace, broken resistor, component pulled out of circuit board, other damage) on the way there.
The relevant pin of the microcontroller is pin 6, which is directly above the top pin of J2, the 6-pin USB-TTL connector.
That trace goes from that pin to resistor R6, which is the first one above the text “Opt RTC Module.” From the right side of that component, the trace is wired (on the bottom side) to a ring-shaped trace around the entire clock face. Since that ring connects independently to all the blue LEDs on line LED6, it is likely that the break is *before* the signal gets to that ring.