How full is each drive? Is there room on either drive to fully contain the data from both drives? If so, move the data from one drive to the drive that has enough space to hold all of the data from both drives, which should leave one drive empty, then move the data you want from the drive containing all of the data to the empty drive.
Another possibility is to use a 3rd drive. Move data from drive E: to 3rd drive, move data from drive D: to drive E:, then move data from 3rd drive to drive D:.