Consider using rSync to pull and push from the server, in combination with source control. That way this wont happen again 
I made a bash script for this, which can be run easily from NPM scripts. See this post and this post. It will even simulate process so you can see what will change without actually doing it. Be aware that rSync will over write files. It’s best used in conjunction with source control so can roll back if you need too.
Alternatively, consider Kirby Autogit plugin, which will push content from live server to a repo.