In some cases, non-orthogonal connections of flanges corners are not actually closed.
Use the Flange connect tool to close the corners.
Select two side faces and the tool will connect flanges.
The Flange connect tool does more than just 45 degrees angles.
When creating junctions, use the Sheet Metal Imprint tool to extend to several side faces.
This will add more edges to your model, giving you more control to modify.