Scope change management practices still apply on agile projects. One technique for helping out with this is to implement a simple spreadsheet listing stories/features added and stories/features dropped with explanations, who raised the change, the date of the request, size (in points) for the change, and what sprint was (or will be) affected.

This will help explain total project variances, but you'll still want signoff on your iteration plans as evidence of approval for the actual scope you addressed on the project.