Losing configuration on update?

as all the questions in the template are irrelevant for this one…:

When I update an App does it overwrite my customized config files? for example i want to modify “settings.json” from transmission. Can it be that an update through the web-interface overwrites my config?

if yes… is there an easy way around it or to get a warning? (If possible I don’t want to setup a ascirpt which always replaces the config after an update)

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