Very puzzled. I rename audio files frequently, as they come in from the recorder with totally useless names as you note. So ... wondering where this goes wrong in your rig.
Have you tried importing (properly) from the Media Browser rather than Finder? Takes no more time, but that seems to get better meta data into PrPro in general.
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I have an H4N but only have old CS6 so can't try to duplicate problem (on win 10). I'm posting mostly to follow this thread, because it boggles my mind.
In the past when putting stuff into PPro from recorders ( H4N or Tascam) I created a bin first. I would name the bin something like Audio-ShootA-date, just something to ID what stuff it is from shoot. Same as renaming all the individual sound files except it's the BIN that names them. Typically for me these are slated things that correspond to the video stuff I also load into a BIN that ID's that junk.
So I link the audio and video simply by counting down. First sound clip = first video clip. I could change the names of stuff in the project panel as I get into the editing stuff, but I don't do it before importing.
The free program ( renamer ) I've used to rename video stuff before imports sometimes. Cause I just let the video recorder default to it's normal naming after starting a new SSD thing ( deleted old files and starting with fresh SSD ).
So I just tell renamer to append (in front of filename) the date I want (which tells me the shoot day ).
Anyway, interesting stuff... good luck and I look forward to what the solution is.
I wonder if it has something to do with FAT32 filename conventions for wav files or something weird like that ?
hehe, I keep trying to work out in my head what might be happening.
If external HD is a little slow maybe user isn't waiting long enough for peak files to be generated...simply waiting a minute or so...so the peak stuff catches up with the Xfer...and all is groovy ??