After testing this with no luck, I've found out that I've to make the changes in the https template! "nextcloud.https.conf.template" that will copy the template to "nextcloud.conf" after reboot.Make changes to nextcloud.conf.template, which I am guessing gets copied to nextcloud.conf after every boot. I did that and it survives a reboot.
By the way: My problem was, that the directive "upstream php-handler" was duplicated in nextcloud.https.conf and nextcloud.conf after the plugin upgrade and nginx was not able to start up. Now, I'm fine