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The regulations state that if you have paper originated documents that you destroy, the copies should be certified. If you have the files electronically, you could use these and not scan and certify, but I would personally assess the effort of just scanning all the documents from paper (certified process) versus scanning some and finding some electronic and filing the electronic ones in between the scanned paper documents!
In addition, you need to be sure that the electronic documents have not been changed over the years.