Add filter to prores file
Your best bet if you want to de-interlace and convert to prores without extra loss in quality is to do both actions at once.  Any re-encode, particularly if the encoding you are working from has had consumer level codecs and/or bitrates applied in the past, will cause (potentially significant) additional degradation.  Your best bet is to minimize the number of re-encodes needed by doing as much processing at the same time as you can and maintaining the highest possible image quality as long as possible in your tool chain.  

It is unfortunately not possible to make many alterations to video without a re-encode.  There's a limited number of actions that can sometimes be taken, but something like de-interlacing is not included in that list.