Yes, on update the rpm deletes the file.
As you said, reinstallation brings files back. And signal-event nethserver-onlyoffice-update makes it work again (on one occassion).
onlyoffice-documentserver reinstallation (relevant actions):
new symbolic_link : /etc/nginx/includes/onlyoffice-documentserver-common.conf
new symbolic_link : /etc/nginx/includes/onlyoffice-documentserver-docservice.conf
new symbolic_link : /etc/nginx/includes/onlyoffice-documentserver-spellchecker.conf
new symbolic_link : /etc/nginx/includes/onlyoffice-http.conf
new symbolic_link : /etc/supervisord.d/onlyoffice-documentserver-converter.ini
new symbolic_link : /etc/supervisord.d/onlyoffice-documentserver-docservice.ini
new symbolic_link : /etc/supervisord.d/onlyoffice-documentserver-gc.ini
new symbolic_link : /etc/supervisord.d/onlyoffice-documentserver-metrics.ini
new symbolic_link : /etc/supervisord.d/onlyoffice-documentserver-spellchecker.ini
new symbolic_link : /etc/supervisord.d/onlyoffice-documentserver.ini