To anyone who's having the "Batch downloading interrupted" error while merging video-only and audio-only files I have found a fix for it.

What you wanna do is:

1. Change "Save merged files in" location to your desktop, e.g. "C:\Users\USERNAME\Desktop"

2. Make sure these boxes are checked:
[ x ] Combine video-only and audio-only files (if FFmpeg is installed)
[ x ] Always download HD quality audio for video-only files
[ x ] Remove download file(s) after successful conversion
[ x ] Always ask for download location
[ x ] Post processing (if FFmpeg is installed): [Extract audio]

And then hit the "Save" button.

Also make sure your FFmpeg Integration is working.

When you start downloading video and audio files you'll be asked where you wanna save those files, save them in your desktop and once downloading is finished the merging process should be done.

NOTE: If you're choosing to download the MP4 versions of the video-only and audio-only then you need to choose a different download location for each one of them (audio-only and then video-only), otherwise you'll get a different error (because both audio-only and video-only versions have the same name, and renaming them will screw up the merging process.)

The WEBM counterpart does NOT have this problem.