I recently renamed a folder in my copy.com folder and caused Copy.com to think that I had deleted it. For example, I had the a folder called "Photos 2013." I installed the copy.com agent on a new computer and it began syncing. Midway through the sync, I wanted to change the folder's name to "Photos 2013-2014". This was interpreted as "Delete 'Photos 2013' folder and all sersver-side contents" and create a new folder called Photos 2014 with the photos in it. So let's say there were 100 photos, and 10 were were synced when I did it. The 90 photos that had not yet been synced would be flagged for deletion on the copy.com server. The 10 photos that actually got synced will remain, in the new "Photos 2013-2014" folder.
All I can suggest to avoid this is don't touch the folders while they are being synced.