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This is what I use to remove the unused files (after, of course, running the aforementioned precious "cleanup" routine)

for wav in *.wav
do grep -q -F "$wav" SessionFile.qtr || rm -fv "$wav"
done

TODO: Get rid of the corresponding .peak files
V0.1 : Hard-crop the wav files, leaving only Nsecs before and after the actually used time (for archiving)