Hi, thanks for your interest in Media Preview.
It won't change any file association and won't change anything on the video files themselves. Media Preview simply reads video files and then stores thumbnails into the system cache.
When you uninstall, everything will be back to default. The "restore default" button is only there for when you installed a lot of video related stuff before and no thumbnail seems to work. It's like your "last saviour" solution for when your thumbnailing system for video files is completely fucked up. So it's doing a reset, and then you can try to re-associate video files to Media Preview.
If you associate Media Preview to flv only, it won't affect other file types as there are still managed by the same previous thumbnailing solution. You can use it with confidence