If you are just changing a video file, the only thing you would need to replace is the video file and the generated .js file. (And for backups sake, the restorable.plist file). Those 3 files would be in your resource folder exported from Hype. You could optionally delete the video file, but there might be some cases where people would have the old generated js file cached in their browser and they would be looking for the other video file.
Not sure you got the best advice? I recommend encoding with a lower bitrate MP4. The MP4 / h264 codec is the most widely supported video codec and is very compressed. Webm is great, but not as supported as mp4. Of course you can do both! But don't remove your mp4.
We've put together a guide to decreasing the file size of your document here: Decreasing load times and optimizing performance: Preparing a Large project in Hype which might help you get things moving faster.