Pete,
I’m thinking that you’re correct in assuming that this probably has to do with After Effects getting tripped up by the file getting swapped but AE using a cached version of the old file. Unfortunately, this isn’t a super common issue, so we’ll probably need to dive deeper into the specifics. I’d like to know a bit more about where the audio files are stored. Is this local footage, or are they being downloaded from a URL? If the source is remote, could you check and see if the “Allow unique downloads for cloud-based assets” box is checked in the Templater Preferences? If the assets are local, I think that getting access to the templater.log file would probably be the best next step so we can see if there’s something obvious happening behind the scenes.
Thanks,
Jeff