Deleted files prevent quitting of Xcode

I was following a tutorial at https://www.youtube.com/watch?v=haZmF3ZYIYc, which near the start has me deleting the art.scnassets folder. Now when I try to run or quite my project I get the error "The document “ship.scn” could not be saved. The file doesn’t exist." Of course, it doesn't exist...it's in the trash. But how do I remove Xcode's knowledge of ship.scn. I have searched the project and can't find anything.

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I'm not sure if this helps but what I did was get on Xcode -> Files -> Open Recent -> Clear Menu. I had a similar issue and that's how I got rid of a file that doesn't exist.

Old question, I know, but I solved the problem clicking in Product -> Clean Build Folder (or shift-command-K).