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Having done something very similar recently I already had a script.

for f in */*/*
do
  destdir=$(dirname "$f")
  tvshow=${f%%/*}
  season=$(dirname "${f#${tvshow}/}")
  episode=$(basename "$f")
  # Get season number
  seasonnum=${season##* }

  dest=$(printf "%s/%s - S%02iE%s" "$destdir" "$tvshow" $seasonnum "$episode")
  echo "mv \"$f\" \"$dest\""
  # mv "$f" "$dest"
done