so...

here at my job, the genius loaders at night keep loading our footage with mxf audio and not omf aiff. the editors have already started to work with it, and we want to transcode it. it seems to be creating new clips, but we want to have it relink to the same master clips that have already been worked with. since we are only transcoding audio, both the old clips and the new clips are linked to the original video media. 

what do we do? i just want all of the clips linked to the new clips and have all the old mxf audio and clips gone!

 Move the new clips to a different drive than the old ones are on and use the unlink/relink function. When re-linking, target only the drive with the new ones.

 Hopefully not pointing out the obvious but have you tried changing the media creation setting in your site settings? This should switch the default format to OMF and keep this from happening again.