I have one problem in a simple file where when changing a material transparency makes a part of the model disappear. After testing, I also found that the glass material behaves not as expected.
Here a view with in ghosted
Here same view rendered with plastic light purple opaque
Same view with same plastic slightly (3%) transparent. Note that a few pieces disappeared on the top.
Same view with glass with very dark blue color. Note no color and the pieces on top disappeared (I think it is almost impossible to see the glass material)
Each piece visible on the view is a block, with a surface in it. The piece that disappears has a block within a block. After exploding one these blocks with blocks (there are three in the view), all three appear - the one exploded and the unexploded two. Note also a different appearance of the sphere seen through the foreground surface, in relation with the next image.
After deleting the exploded blocks, the other two (unexploded) disappear from the rendered view - they are still there.
I suspect it has something to do with the blocks within a block, but it is strange that only has a problem in transparent materials and it is stranger that they all appear when one of them is exploded.