I did a quick fix to make it work (in Linux Mint), as per the below

In file:
/usr/share/soundconverter/python/soundconverter/batch.py

locate the below text and add the line shown below ending with <<< (with
out the <<<).


def prepare_files_list(input_files):
    """ Takes in a list of paths and returns a list of all the files in those
    paths. Also converts the paths to URIs.

    Also returns a list of relative directories. This is used to reconstruct
    the directory structure in the output path if -o is provided. """

    # The GUI has its own way of going through subdirectories.
    # Provide similar functionality to the cli.
    # If one of the files is a directory, walk over the files in that
    # and append each one to parsed_files if -r is provided.
    subdirectories = []
    parsed_files = []
    for input_path in input_files:

        input_path = input_path[7:]   <<<

    # accept tilde (~) to point to home directories

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https://bugs.launchpad.net/bugs/1858881

Title:
  Batch mode doesn't work in version 3.0.2

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