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Stick them in a file called Snippets. This has one function and one function only: to make it easier to excise all the stuff that does not belong in your story. Tell yourself that this is good stuff and one day you will go and find a way to use it in something else. You won't, but that's okay. The point is simply to ease the pain of removing it from the story that it does not belong to. It does not matter what you do, it only matters that you do something so that your story just has the scenes that belong to it, not the irrelevant scenes that you fell in love with. 

Here's the truth of it. You learned to write good prose. Its easy once you learn, and you can churn it out about as fast as you can type. You learned to write good scenes. That takes a little longer, but once you learn you can turn out a good scene on demand. The hard thing is constructing long form stories. 
That will be the study of a lifetime. Sacrifice everything to that. 

In your next story, if you need a good scene, you will write one. You are good at that now. No need to go looking back in your snippets file and hoping you will find something useful. You don't need to. You are good at writing scenes now and you will write a brand new scene that is just the scene this new story needs. 

If you end up writing some good scenes in this new book that don't turn out to work for the story, by all means add then to the snippet file. That is what it is for. You will never use them again. It doesn't matter. All that matters is to get them out of the story that they don't belong to.