I had a similar issue with a horizontal section plan through a house model getting flipped upside down after I used the scale tool to mirror the model right to left. I noticed that the section plane arrows went the wrong way and the cut showed the wrong half of the model. I was unable to select the shown geometry correctly. In Layout, the object snap feature wouldn't select geometry that wasn't right on the section cut. The Sketchup scene with the cut in question kept breaking: it would show the wrong half of the cut from time to time, and I would need to switch it back.
My solution: I noticed that the axes of my house got flipped along with the house model when I used the scale tool. I used: Tools>Axes to change the axes of the house back to the default configuration. This change made my section plane and section cut work normally again.