@glutanimate this is caused by IOE using a combination of add_file() and writing files directly into the media folder - the latter are not getting picked up due to the dir mtime being the same timestamp. I’ll trial a change that will avoid this in .55, but you may still want to address it for previous Anki releases.
Thanks for the heads-up! The add-on should account for that normally (by using a fairly silly approach - writing a dummy file to update the mtime). But that must have broken with 1.4.0. Added to the issue tracker here and will look into it.
The issue here is a bit different - the repro steps above cause new files to be added as well, which would normally trigger a scan for changes, but that doesn’t happen as the directory timestamp was just updated by a call to add_file. As the resolution is to the second, the subsequent direct writes don’t cause an observable difference in the timestamp.