Found a potential answer while writing the question: Menu--> Analyze - analyze a document that has the unwanted error flagged. Then in Inspection Results, click the wrench and uncheck the Inspection you do not want to run. In my case this was under CSS, uncheck Unknown file or directory.
I also noticed this icon of a guy wearing a bowler hat with his back to you (wow) that, when clicked, can turn off redlining for a very specific error instance. This appears to also apply to any other document in the project with the same exact error. That's a bonus since I know the paths that are supposed to be used and just turn the error off for them and detect incorrect paths in my strange dev setup.