When we make updates, we usually make changes in many files and it’s hard to keep track of the exact code and files names.
Since your changes are minor, this is what I would recommend.
Make a backup of the theme locally, on your computer.
Update the theme files to latest version.
Then add your changes again.
This time, you can try add them in a child theme. Moving .js and .php changes in child theme requires you have some WordPress development knowledge, but you seem like you know your way around with coding. In the latest theme pack you will have the minimum required to start the child theme and a read me file with the instructions and link to wordpress child theme documentation.
We will soon release 2.03 (it’s a matter of days), then we will add 2.04 with WPML support.