Ok, that sounds like you have/had a much more serious problem on your hands. It definitely should only ever replace individual files that don't match the server versions. Anything else would be throwing money down the toilet on Valve's part.
The more likely issue for other people here is that the videos/lua files would get re-downloaded if deleted. It still shouldn't happen unless you verify your game cache in Steam, but it is possible.
If it does happen then I'd recommend using unique filenames on the custom videos so that they don't replace the originals. That way Steam ignores them (it doesn't see or care about extra files) and is happy that the originals are still there. Then copy the relevant customised lua files somewhere safe and simply paste them back in after the patch. It'd be about a 10 second job.
It is quite a lot of work though. It would be much better if we just provided powershell or python script that does it after every cache check together with videos. So you could throw the script into the folder, get yourself a nice shortcut on the desktop and forget where your installation is placed.
I just speculate as I'm no steam expert, but maybe there also is some way to run a predefined script every time the game starts? It could check your files configuration, run AHK and so on, so that you could press only one button.