We are looking at moving a some documents into a SharePoint 2010 document library.
Is there any way to set the starting version number for each document?
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No, this is not directly possible. You will need to upload and delete some dummy versions to do this. For example if you need the starting version number to be three simply start by uploading two small dummy versions and then delete them again. Performance can of course become an issue if you have many files with high version numbers.