The same happened to me just minutes ago. 
When I left the office, u1 synced to the server. Now I started my notebook and 
apparently all the new latex files from  a days work on the u1 server have been 
overwritten with the two days old files from the notebook. No .conflict ending 
or anything. I just found out because I was missing lots of text I had written 
today. Other files, such as .pdf and .rtf files are not affected - they were 
correctly downloaded to my notebook. Only latex files and the whole kile 
project file is overwritten. Luckily they are still  on my computer in the 
office.

I have seen other bug reports regarding problems with latex files which
lead to 100% CPU load because u1 continuously hashes. Dont remember the
Bug # though.

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https://bugs.launchpad.net/bugs/575548

Title:
  ubuntuone overwrites a newer version of a file or creates a conflict
  version

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