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Can we use SharePoint Online (Office365) Client Object Model to backup site structure and data? we need to make an application to backup/restore our SharePoint 365 Online site. Is it feasible to backup/restore the whole site data and structure? what are the limitations?

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Yes, the CSOM API can do this with programming. Additionally there are 3rd party solutions that can out-of-the-box replicate / mirror the data to local on-premise applications, e.g. databases, the "Cloud Connector for Office 365".

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By using ClientOM you aren't able to impersonate into a system account so you have to ensure that the backup progress will be started by an user having access to all the data.

You can access all the lists and libraries using the ClientOM but I think you should consider lookin at something like this http://www.avepoint.com/sharepoint-online-migration-docave/

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