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Welcome adnion,
I had a similar situation: I dont know Traefik, but maybe this will work for you too…
I had already run letsencrypt certbot on a debian machine.
I then used this to start my x86 Docker container:

docker run -d -p 4443:4443 -p 443:443 -p 80:80 -v ncdata:/data --name nextcloudpi ownyourbits/nextcloudpi-x86 $sub.domain.tld

I then used

docker exec -it nextcloudpi ncp-config

to run nc-letsencrypt (which failed, as expected, because port 80/443 are not available, I used DNS to validate. But it ensured that inside the docker the PATH to /etc/letsencrypt/live gets created)
I then copied the existing folder holding the cert and key with:

sudo cp -avr /etc/letsencrypt/archive/sub.domain.tld /var/lib/docker/volumes/ncdata/_data/etc/letsencrypt/live/

Edit NC’s apache config to change the name/location of cert and key files:

sudo nano /var/lib/docker/volumes/ncdata/_data/etc/apache2/sites-available/nextcloud.conf

and reload Apache2:

docker exec -it nextcloudpi bash
service apache2 reload

You can also disable HTTPS if you are going to use a reverse proxy with SSL (nc-httpsonly option)

Still works for me, but I do have to renew it manually every 90 days tho. If you create symbolic links, as does letsencrypt, no need to copy them over, just reload webserver.

NCP is v0.67.11 presently, do you have nc-autoupdate enabled?

Did you ask/consult Traefic forum/docs?