I noticed this same phenomenon with all three of the auto-syncing cloud storage services I tested: Apple's iCloud, Google Drive, and Microsoft's SkyDrive.
During testing, all three of those services incorrectly deleted files when the cloud service got confused about synchronization. So for the particular application I had in mind, I wasn't able to use any of them and had to write scripts to handle the synchronization myself.
During testing, all three of those services incorrectly deleted files when the cloud service got confused about synchronization. So for the particular application I had in mind, I wasn't able to use any of them and had to write scripts to handle the synchronization myself.