Does Automator keep a log of all changed files?
Automator doesn't keep a log file, if you didn't include some logging routine in the action itself.

You should be able to find all falsely renamed index.html files by checking the modify date of superior folders: search for all files with the name index.php and check if the modify date of the superior folder is the same as the execution date of the Automator action. If the modify date is the same, the file (not located at the "specific" folder) was renamed unintentionally. If the modify date of the superior folder is earlier than the Automator action execution date the file wasn't renamed.

To get all folders containing a file index.php quickly, enter:

sudo find / -type f -name 'index.php' |sed 's#\(.*\)/.*#\1#' |sort -u


To get a list of folders sorted by modify date with ls use something like this:

ls -dl $(find / -type f -name 'index.php' |sed 's#\(.*\)/.*#\1#')


The last command doesn't work for paths containing spaces!