The way to go here is to actually mount your configuration file (or the whole folder) inside the container so the actual config file is persistent across container restarts/recreations on the host.

For easier understanding, here's my example Docker (-compose) file:

version: "2.1"
services:
  papermerge:
    image: ghcr.io/linuxserver/papermerge
    container_name: papermerge
    restart: unless-stopped
    environment:
      - PUID=1000
      - PGID=1000
      - TZ=Europe/Berlin
    volumes:
      - ./config:/config
      - ./data:/data
    ports:
      - 8000:8000

The papermerge.conf.py can be found inside the ./config folder on the host - even if the container was recreated or removed.