Batch Renaming with Adobe Bridge - How to change incrementing numbers "(1)", "(2)" with duplicated

Here is a bash script that does exactly what you want: replaces ' (n)' with '_n'. Just run it within the directory where all the files are located. Be sure to change the script (call it rename.sh, or whatever) to executable permissions with command: chmod u+x rename.sh

#!/bin/bash

shopt -s nullglob
counter=1

for file in *' ('*')'*; do
if [[ $file =~ (.+)\ \(([0-9]+)\)(.+) ]]; then
base_name="${BASH_REMATCH[1]}"
extension="${BASH_REMATCH[3]}"
new_name="${base_name}_$counter$extension"
mv "$file" "$new_name"
((counter++))
fi
done

You would need to either avoid duplicated filenames or run another Batch Rename to change the offending characters.