When updating an installation through apt (which is the openhabian way), the underlying mechanism will ensure not to overwrite configuration files without asking for permission. The default behavior is not to overwrite, and this is not changeable by repo, but only through apt configuration.
But you could always choose yes and the original configuration will be saved. When choosing No, the new file will be saved, so, you only have to find the new files…
Try to find files named to <some name>.dpkg-dist, change <some name> to <some name>.dpkg-old and change <some name>.dpkg-dist to <some name>
Hmm… as I did not use openHAB under Windows for a very long time (since 2012…) I’m running out of ideas.
Maybe you should backup your configuration and reinstall openHAB, then move your backup to the fresh installation.
Keep in mind that you must not simply replace all files from userdata\etc but only those which are needed (this will be the tricky part…)
I too have the same problem with the logging and read your post. I don’t have the /var/lib/openhab2/etc/org.ops4j.pax.logging.cfg.dpkg-dist file at all.
Do you have a suggestion what I need to do