Doing something "from scratch" means that you do it from the very beginning, without having some parts of it done for you.
For example, baking cookies "from scratch" means combining flour, eggs, sugar, etc. to make the cookies (instead of buying pre-made cookies or frozen cookie dough):
Want a cookie? I made it from scratch!
"Starting over from scratch" means doing something again from the beginning. You can use this phrase if you did some work but now you have to do it over again because you lost it or because there was a problem with the first version.