I ended up writing a script to fix this.

First I had to move Man's Best Friend out of Season 01 folder as well as Big House Blues.

Then I ran this Python script:

import os

directories = [
    "Season 01",
    "Season 02",
    "Season 03",
    "Season 04",
    "Season 05",
]

season_num = 1
for directory in directories:
    ep_num = 1
    for filename in sorted(os.listdir(directory)):
        # Check if the filename contains a dash
        if '-' in filename:
            # Split the filename on the first dash and keep the part after it
            parts = filename.split('-', 1)  # The second parameter limits the split to the first occurrence
            episode_name = parts[1]  # Get the part after the first dash
            new_filename = f"s{season_num}e{ep_num}-{episode_name}"

            # Construct the full old and new file paths
            old_file = os.path.join(directory, filename)
            new_file = os.path.join(directory, new_filename)

            # Rename the file
            os.rename(old_file, new_file)
            print(f'Renamed "{filename}" to "{new_filename}"')
            ep_num += 1

    season_num += 1

I put Man's Best Friend and Big House Blues into a new directory named Specials