Answered by DazWilkin

I think file systems aren't shared between jobs (create_zip, google_cloud_services). You may want to prove this and consider moving the actions/download-artifact to google_cloud_services.

Working code

name: CI Workflow

on:
  push:
    branches:
      - main

env:
  PROJECT_ID: "flights-429420"
  BUCKET_NAME: "flights-cicd-bucket"

create_zip:
    runs-on: ubuntu-latest
    needs: test
    steps:
      - name: Checkout code
        uses: actions/checkout@v2
        
      - name: Install zip
        run: sudo apt-get install zip

      - name: Create jobs.zip
        run: |
          cd app
          zip -r ../jobs.zip jobs

      - name: Upload zip file
        uses: actions/upload-artifact@v3
        with:
          name: jobs
          path: jobs.zip


  google_cloud_services:
    runs-on: ubuntu-latest
    needs: create_zip
    steps:

      - uses: actions/checkout@v3

      - name: Download zip file artifact
        uses: actions/download-artifact@v3
        with:
          name: jobs
          path: ./downloads
      
      - name: Authenticate with GCP using Service Account
        uses: 'google-github-actions/auth@v2'
        with:
          credentials_json: ${{ secrets.GCP_ACCOUNT_KEY }}
      
      - name: Setup GCP CLI
        uses: 'google-github-actions/setup-gcloud@v2'
        with:
          project_id: ${{ env.GCP_PROJECT_ID }}
          install_components: 'gsutil'
      
      - name: Create GCS bucket if not exists
        run: |
          if ! gsutil ls -b gs://${{ env.BUCKET_NAME }}/; then
            gsutil mb -l EU gs://${{ env.BUCKET_NAME }}/
          fi
      
      - name: Upload files to GCS
        run: |
          gsutil cp ./downloads/jobs.zip gs://${{ env.BUCKET_NAME }}/jobs.zip
          gsutil cp app/main.py gs://${{ env.BUCKET_NAME }}/main.py
          gcloud storage objects update gs://${{ env.BUCKET_NAME }}/main.py --content-type=application/octet-stream

You could use the following Github Action to have the same files in the destination as in the source:

name: Copy files to GCS
on:
  push:
    branches: [main]

jobs: 
  copy-files-gcs:
    name: Copy directory to GCS
    runs-on: ubuntu-latest

    # Add "id-token" with the intended permissions.
    permissions:
      contents: 'read'
      id-token: 'write'   
  
    steps:
    - name: Checkout
      uses: actions/checkout@v3

    - id: 'auth'
      uses: 'google-github-actions/auth@v0'
      with:
        credentials_json: '${{ secrets.GCP_CREDENTIALS }}'

    - name: 'Set up Cloud SDK'
      uses: 'google-github-actions/setup-gcloud@v0'

    - name: 'Use gcloud CLI'
      run: 'gsutil -m rsync -R -d kavach gs://<your-bucket>'

The key for syncing the files in destination folder as you are looking for is the -d flag for rsync which deletes the files in the destination that are not present in the source.