I have a series of circles that I wish to clip with a shape on the layer above. All of the circles and joined lines are all joined paths, and can be clipped using a simple square shape. But when the shape becomes more complex they won't clip, and the layers dissappear. When checked the complex shape is also a good joined path and filled shape. See images below: A Square works, but not the next shape. The next shape produces no clipping and basically deletes the contents of both layers. Why?
The second is a compound path… much more complex. Have you tried a transparency mask? I don't know if you run into similar problems.
Another question: Could the circle pattern be designed as an effect, instead of actuall lines? I wonder if this would simplify the file and allow the compound mask to work?
Perhaps you are doing this already, but if you assign a "Transform" effect to one circle, you can create the pattern you have. Then it can be changed easily.
If you have a case with overlapping top shapes, you may need Pathfinder>Unite rather than Object>Compound Path>Make, or a combination, but you can also just Group the paths, overlapping or not, and use Transparency flyout>Make Opacity Mask with both Clip and Inverted ticked (you can use that in the present case, too)