Hi,
Your issue looks like something our customers are already seeing Files are getting deleted from creative cloud
Please send in your log files so we can be sure about this.
The logs are located at
Mac:
The log file can be found here:
<Mac Hard Drive>/Users/<username>/Library/Application Support/Adobe/CoreSyncSync/CoreSync-YYYY-MM-DD.log
(where YYYY-MM-DD indicate the date of the last log)
Note: The Users Library user folder is hidden on starting with 10.7 or later
see http://helpx.adobe.com/x-productkb/global/access-hidden-user-library-files.html
Windows:
The log file can be found here:
C:\Users\<username>\AppData\Roaming\CoreSync\CoreSync-YYYY-MM-DD.log
(where YYYY-MM-DD indicate the date of the last log)
Note: The AppData folder is hidden by default this doc shows how to show it if needed
http://helpx.adobe.com/x-productkb/global/show-hidden-files-folders-extensions.html
Please zip them up and send them to SyncForum-Communication@adobe.com with this forum URL in the email.