MPG To ProRes Loses Audio - Looking For Best Solution

I'm starting a doc project that will use a lot of old DV footage in MPG. I'm converting all files (other formats as well) into ProRes 422 LT before I begin. Most of the MPG files transcode in Media Encoder fine, but some lose audio, which, I asume is because they are Dolby AC3, which I understand is no longer supported by PP. 

As a workaround, I have found that if I convert the problematic clips to MP4 in Handbrake (which doesn't support ProRes), I can then import them and use the audio to replace the blank audio in the ProRes clips. I would then export that clip as ProRes and reimport them so that the clip will retain the correct audio track for all future use. 

I'm wondering if there is an easier way to replace audio in clips without the circuitous round trips. Is there a way to replace the audio in a clip within PP? Some way to unlink the audio and replace it? 

Thanks.