native footage AVCHD and Premiere Pro CC 2015

but what I'm saying if I'm rename my files in premiere and make a proxy out of the renamed native footage and then link back to native after using proxy the renamed files reverts back to 0001.mts and so on rather than the name I gave them
 
how do you trasncode your rough cuts without losing all the crossfades and titles when you transcode to ProRes?
Rough cuts are just that, no FX transitions, no graphics, just straight cut edits of shots to be used in each scene that have to be graded to match. Final edits with FX and graphics are done with graded Cineform or Prores digital masters.
Rough cuts are very loosely trimmed subclips of individual shots with plenty of head and tail length for FX later. I organize them in bins by scene and use the "make edit from bin contents" to auto assemble them. Often can be done in less time than it would take to watch all the raw footage through in real time.
 
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