Renaming MXF files and pulling them out of their file structure

My company's workflow necessitates that we pull mxf files out of the file structure and rename them. I know this is a big no-no, but with CalibratedMXF it is no problem.
My proposed workflow was to use Prelude to locate the mxf files from where they are backed up on my drive, ingest them, copy them to a new location, and rename them.
In attempting this process, however, I am realizing that Prelude will not pull mxf files out of their file structure. It copies the entire mxf folder structure to the new location, and renames the media only in Prelude (the clip name, not the filename).
The only way to get Prelude to rename and discard with folder structure upon copy to new location is to check the 'Transcode' box and transcode the media.
I want to work natively in mxf, I do not wish to transcode or rewrap.
My workaround was to transcode the files to the exact same setting: MXF Op1a with preset 'Match Source (rewrap)'
However this process simply forces Prelude to crash.
Any suggestions on how I can batch copy and rename mxf files, instead of going through each level of folders for each clip and dragging the file out and manually renaming one by one?
Prelude CC
OS X 10.9.5
3.5 GHz Intel Core i7
files are C300 MXF Op1a MPEG-2

Hi Kaye,
Sorry if I missed this in your description of the problem, but what device is generating the MXF files you are attempting to rewrap? Also, when Prelude crashes, which it should not do obviously, does the crash reporter launch? If so, can you copy or attach the report into a reply?
Thanks!
Michael

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