There are a couple of “flatten” plugins but no native command to “flatten” your model. SketchUp Pro users can export a 2D plan view to DWG or DXF format and re-import that into SketchUp.
Besides lines that are non-planar, also lines that are on a face without actually cutting it sometimes display these “z-fighting” symptoms.
You can also post your file for forum members to take a look at it.
Anssi