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I would suggest to use the powershell with SharePoint CSOM and write the custom code to extract the data in to your external database as needed. Pls refer the below link to get an overview on CSOM with powershell. Reference Link


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200 GB is the maximum size recommended for each content database. since you already have 200GB of files, I would recommend enabling Remote Blob Storage(RBS). Enabling RBS will reduce the load on SQL server and also keep the BLOB files outside the SQL database. which mean all the uploaded files are externalised. Check the following URL if you want more ...



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