Trancoding RED EPIC RAW to DNxHD...Multiple Files

Transcoding RED EPIC RAW files to DNxHD using Prelude and AME. Some .RDC folders have multiple .R3D footage that is the same. Each is aprox 4gb.  Its the same footage, Timecode etc. When I transcode through AME, the new files are much larger, depending on how many repeat files are in each folder. Usin AME Preset DNxHR HQ UHD 23.976 and Format DNxHR/DNxHD MXF OP1a.