Who does modify my XML-Files on iCloud, if its not me?

Hello All,
I am using iCloud to synchronize my Scrivener projectfiles between my Macs. Scrivener is a writers software, storing projects as packed XML-Files (*.scriv).
Using iCloud Drive to store my projects I have faced several times an unknown process is "unpacking" those files and stripping them into their directory structure without me having asked for that. Obviously, My writing projects are messed up and Scrivener can't read the files anymore. I wonder what unknown process does change the files I stored on iCloud Drive? Why is my data being modified?
Any hint would be appreciated.
Regards,
Thomas
This is how it looks when I drop the *.scriv Files onto iCloud-Drive:
This is how it looks after a while. It looks like all Files have been modified by a process, nearly at the same time.

Hi Taunda
When you went through the iOS 6 set up - did you see the option to restore?
When you go through Setup Assistant on a new iOS 5 device, choose "Restore from iCloud Backup" and enter your iCloud account and password. You will see the three most recent backups for each of the devices on which you enabled Backup. Choose which backup to restore from.
After your device restarts, your settings and accounts are restored and Backup starts downloading your purchased music, movies, TV shows, apps, books, Camera Roll, and other content.
Note: You may be prompted to enter the passwords for all accounts enabled on your device. You may also be prompted to enter the password for for any iTunes, iBookstore and App Store accounts for which iCloud Backup is attempting to restore content.
A progress bar will appear underneath the apps that are being downloaded. To prioritize the restore of a specific app, tap its icon. Restore will attempt to download the same version of the app that you had installed previously. If that version is no longer available, the latest version of the app will be restored.

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