The server is provisioned with standalone/configuration/logging.properties
file. Then this file is updated (let's say by the user, standalone.sh modify this file after first start). Then during the update, this file is not changed (hash file from the new installation is the same like a hash file from the original installation, galleon can check it). But the galleon prints "warning about the conflict and create new logging.properties file.

Is there some reason why Galleon can't find out that there is no changes in this file during the update?

This behaviour is according to the documentation: https://docs.wildfly.org/galleon/#_application_of_user_changes_to_the_updated_installation_state -> Table 14. User-modified file -> Found and is different from the resulting file modified by the user -> .glnew

But this behaviour looks strange.