Updates should never overwrite favicon, background or logos but each time I've updates, this has happened.
That would be very amateur looking on any high traffic site.
Can this behavior be changed? Maybe put those things in the DB as blobs.
@Maurice, it means that if you save your folder before the upgrade, you can re-copy your files back to the updated folder. Or, you can remove the images folder from the update.
Either way is a lot to keep track of and it's easy to make mistakes when having to do such things manually.
If the images folders is deleted from the download update, can it just continue to use the image folder and files that are already uploaded ?
The problem is that this is tedious and could be overlooked during an upgrade. Logos and login page images should easily be put into the DB so no one has to think about this.
I hope you'll consider doing this.
The only way to avoid this in future is to download update and delete images folder from the theme you are using then replace files. Of course replacing the files override those changed things.