Need to override this automation if the light turns on manually

Configuration
7

Using the context variable, start a timer when the switch is turned on manually. Just FYI, if you are using a helper to change device type of a switch to light, it is best to use the switch entity in the first automation.

alias: Kitchen Lights Manual Timer
description: ""
trigger:
  - platform: state
    entity_id: light.kitchen_lights
    to: "on"
    variables:
      id: "{{trigger.to_state.context.id}}"
      parent: "{{ trigger.to_state.context.parent_id }}"
      user: "{{ trigger.to_state.context.user_id }}"
condition:
  - alias: Test if triggered by physical device
    condition: template
    value_template: "{{ (id!=None, parent, user) == (true, None, None) }}"
action:
  - service: timer.start
    target:
      entity_id: timer.kitchen_lights

Modify your original automation to not turn the lights off when the timer is running and to trigger when the timer finishes.

alias: Autolights - Kitchen + Ut
description: ""
trigger:
  - type: present
    platform: device
    device_id: e1ad7b06f6483100fdc1ded7bea6659e
    entity_id: 2875b2fff8b63f52cfc657cefa2ca682
    domain: binary_sensor
    id: Motion detected
  - type: not_present
    platform: device
    device_id: e1ad7b06f6483100fdc1ded7bea6659e
    entity_id: 2875b2fff8b63f52cfc657cefa2ca682
    domain: binary_sensor
    id: Room empty
  - platform: state
    entity_id: timer.kitchen_lights
    to: idle
    from: active
    id: Timer finished
condition: []
action:
  - choose:
      - conditions:
          - condition: trigger
            id: Motion detected
          - or:
            - condition: sun
              after: sunset
              after_offset: "-02:00:00"
            - condition: time
              before: "00:30:00"
        sequence:
          - service: light.turn_on
            target:
              entity_id: 
                - light.kitchen_lights
                - light.utility_room_light
      - conditions:
          - condition: trigger
            id: 
              - Room empty 
              - Timer finished
          - not:
              - condition: state
                state: active
                entity_id: timer.kitchen_lights
        sequence:
          - service: light.turn_off
            target:
              entity_id: 
                - light.kitchen_lights
                - light.utility_room_light
mode: single
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