Mac – Software to backup recently modified files in few directories

There is no way to know for certain exactly which files were deleted. There's no list stored, no trash can, this is unix (well BSD) and you don't get any nice second chances with rm -rf

As you have seen though, you can infer what might have been deleted first by observing the rm command's behaviour.

I created a folder with a few subfolders, including some with a period at the beginning of the name and threw a few files into each.

The order is always alphabetical with the hidden, period prefixed directories getting deleted first.

If you compare a backup with your directory structure, once you have moved through alphabetically and started to find files in the backup that are still on your main drive, I think you can rest assured that you haven't missed any other files.

If you have Time Machine enabled as a local store option or backing up to an external drive, then that file would be backed up - perhaps several versions and stores.

The filesystems Apple ships do not have any archive or redo, so you would need to have backed up your application. It's odd that it would store things in the application bundle and not the user home folder. Did you check that perhaps it moved the files to the proper location as part of an update?