/etc/ files from Debian package disappearing

Dear Yunohost dev team,
I’m providing a new packaging of Prosody based on the official Debian package which provides default configuration files in /etc/prosody/ . It seems that these files sometime (quite often?) disappear during the installation ( missing /etc/prosody/prosody.cfg.lua after installation · Issue #11 · anubister/prosody_ynh · GitHub ).
I could provide a workaround (providing again the conf file via the ynh app), but I’d like to understand if I did something wrong or if /etc/ is somehow protected against configuration files not explicitely declared inside the installation script?
Unfortunately I could not find similar existing apps based on a Debian package AND using the default configuration file.
Many thanks for your hints!