HD P2 Transcode issues

I'm working in 1080/30P HD on Avid MC Adrenaline 2.8.3. Using DVCPro P2 media, I'd like to transcode to DNx145 on the way into the editor. Every time I try the audio isn't included with the new clip. To be exact, it shows audio tracks, but there's no sound. So I decided to import the old fashioned way by copying the MXF files to an empty MXF/2 folder on the media drives and transcode from there. That works fine... video at DNx145 and audio with it. When I delete the original DVCPro HD media from the drives however, my audio linked to the transcoded footage disappears. Am I missing something about how transcodes work? Doesn't transcoding duplicate the audio automatically and relink it to the mew media?