[bug] Changed configuration files get overwritten during updates

Each RPM specifies (per spec file), if it overwrites (default), backups or retains individual configuration files when updated.
This is how RPM works (i.e., on all Linux distributions utilising RPM).

So you may address this as an issue for the specific RPM you had issues with (e.g. at git.sailfishos.org).
Side note: Usually the RPM's (spec file) authors had reasons to set a specific behaviour (or not) for a configuration file.

The overwritten files belong to droid-system-vendor-voyager package. I'll try to make a pullrequest when I'll have free time, I see no problem with config files marked config(noreplace), since files won't be owerwritten only if they were changed.