You have edited the DPXs into another sequence and exported. Therefore the logic dictates that they will be give the timecode from the record sequence.
To reassemble the edit in Flame after export the DPXs, you export the accompanying EDL. When you reimport the EDL, there should be an option to use record time codes as source time codes. When this option is enabled, you should be able to assemble the EDL based on the timecode of the exported DPX files.