“I now duplicated all of the audio files in the Finder and renamed them by shot, take, etc., but of course, this doesn’t change the names of the files in the timeline”
DUPLICATING the clips was a mistake
if you did not dupe he clips, the timeline instances of the clips would have followed your name changes
well, they SHOULD have if they had the proper master / affiliate relationship
“Is there a fast way to do this..relatively fast?”
start again.
as you have already made most decisions about what to call the clips,
doing it a second time should be a bit quicker
if you want to you can simplify the job by only working on the clips that are in the timeline.
i would advise you to COPY the edited sequence into a NEW PROJECT
select the sequence in het b rouser, and got TOOLS MENU > Create Master Clips.
this will give you just the used clips, plus the maser affiliate relationship would work.
nick