So said the mystic sage Obi-Wan Kenobi in Star Wars: A New Hope (1977).

This applies to your writing just as much as any real-life situation.  In real life, your instincts can either save you from a bad situation or encourage you to take a leap of faith.  

When it comes to your writing, only you as the writer can know if a particular scene needs to stay, even if you aren’t able to articulate why.  Trusting that scene’s place in your story is very important.  Your job as a writer, then, is to find and tease out the threads that will ultimately reward that instinct and faith.

Sometimes, those reasons will come up easily.  Many times, it will require walking away from the project for awhile, allowing it to percolate in the back of your mind.  And other times, it may require a creative project in a different medium to distract that focus long enough to allow the ideas to flow through you. 

Once you find those little connections between that scene and the rest of your story, it’s just a matter of threading them into the body of your work.  It will be time-consuming and more often than not a little frustrating, but the end result will be worth it.

Trust your instincts and keep the faith.

The story, through you, will work itself out.