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I used Ubuntu One to upload my Documents folder and some other folders to one.ubuntu.com. All documents got uploaded.

But does Ubuntu One re-upload documents when they change on the pc, or do I have to click the locally box? I tried clicking it yesterday, and it overwrote my more recent pc files with older version in the cloud. Fortunately, I had backed them up.

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You need to have the "Sync locally? []" check box checked in the control panel, in order to keep the folder in sync, yes. If it is unchecked, then Ubuntu One is not keeping those files in sync locally.

However, if it overwrites newer files with the old ones, that is a bug and you should open a bug report on Launchpad against ubuntuone-client about it:

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If this is the Ubuntu One client running on Ubuntu, then it's preferable to start the bug report with ubuntu-bug. This explains how to report bugs in Ubuntu packages. –  Eliah Kagan Jul 12 '12 at 15:46

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