First suggestion: even though things are weird, make a complete back-up of your site as it currently is....for just in case.

Second:You may not want to over write config files or the cgi-bin (espcially if you have the progress bar enabled). Even if you do, you can refer to your back-ups for the settings. ;)

Config files are located in the includes directory config.php and includes/settings has the video convert files there.

I had someone the other day contact me because suddenly the embed code that appears on the view video page wasn't working. I uploaded fresh copies in binary of the root .php files and all the js files (since I wasn't sure where the problem was coming from) and his site worked fine after that.

But always always always make regular back-ups of your sites! Especially when everything is working fine and running smoothly so that in the event something blows up for some reason, you can just do a re-upload.