While I agree with @Anshul_Namdev, let’s just take a step back and make sure we are not overlooking something simple.
Would you mind sharing your docker-compose snippet? First thing we’d want to make sure of, is that .env value is being propageted to your Docker container.
When you have the url only in .env variable and after restarting:
docker compose down docker compose up -d
what is the output for: docker compose exec n8n printenv | grep WEBHOOK_URL ?
It may be helpful to take a look at these posts as well. I’d start here and dive deeper, once we can exclude the simple issues.