Bad normals
This is an issue I hit whilst revising Lund Church.
A model is made up of polygons, and each polygon has a front and a back. In Blender it is not obvious which is which, though Blender does track it. And occasionally it gets it wrong, and a section of mesh is, in effect, inside-out. When you try to print out, there is just a hole there.
In the image below you can see some of the stones to the left of the windows are not just missing but also caused holes in the superstructure.
Microsoft 3D Builder does not spot it, all looks good in there. But Chitubox does. It will not actually say anything or stop you producing a bad file, but it does highlight bad bits in your model. In the image below, all that roof is wrong, the right side of the arches, a part of the cross at the end of the roof, and some stones in the tower. All are shown in a much darker colour.
So what are normals?
Behind the scenes Blender creates a vector (essentially a line) that starts from the centre of the polygon and extends out at the front, at a right angle (i.e. normal to) the plane of the polygon. You can have Blender show normals so you can check which is the front. I like to give them a length of 0.3.
This is how it looks in edit mode, X-ray turned on, with face select. The cube on the left has the normals pointing inwards - it is inside-out and will not print. The cube on the right is good, with all the normals pointing outwards.
Of course, if your object has a hole in it, the normals round the hole need to point into the hole.Addendum: After upgrading to Blender 4.0, I can no longer find the show normals option on the viewport overlap; the entire bottom half of the menu is missing. However, I discovered a better way to do this. On the same menu tick "Face Orientation". This is not restricted to Edit Mode, so you can check an entire model at once. The front of each face will be blue, the back will be red.
What do I do about it?
Once you have identified bad normals, it is easy to correct them. Just select the offending faces in Edit mode, and flip them by pressing [ALT]-N, and selecting "Flip" from the menu.
The tricky bit is finding them all and selecting just the right ones.
One thing to try is, in Edit mode, with Vertex select, do Select by non-manifold.
This can pick up other issues, but might pick up the ones you want and you can just flip them.
Why does it happen?
This is the big question. This church is the only model I have had it happen on, but it happened numerous times. Why?
I do not know for sure, but I think mirroring is a factor. What mirroring does is set one of the scale factors to a negative number. That is fine generally, but if you join a mirrored object to another object, the normals on the mirrored object will be reversed. I have reported this as a bug, but I find it odd no one has found it already (it was also an issue in 3.5).
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