Once I fixed my other problem with my push to rooter script which copies the letsencrypt cert to my rooter and to my pdc, I created an additional virtual host on nethserver and a corresponding dns entry on my hosters dns editor to temporary to circumvent the problem of having requested certificates too often and added the additional host.ourdomain.tld to the letsencrypt certificate request. I then moved the archive, live and renewal folders under /letsencrypt/ like described in this post and re-requested a new certificate. -> solved
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