Clipping masks in Illustrator aren't the same as in Photoshop. In fact, they are sort of reversed.
In Photoshop...
- Layer containing content to be clipped
- Layer defining boundaries of clip area (text layer, shape layer, etc)
Then you Option/Alt-click between the layers and the top layer is clipped to the bottom layer.
In Illustrator....
- Shape defining clipping mask
- Content to be clipped
Then you select both objects and choose Edit > Clipping mask > Make
and the bottom object is clipped to the shape of the top object.
The difference is in Illustrator you need the shape defining the clipping mask above whatever is going to be clipped.
If you want to retain the base object appearance and add an additional clipping mask on top of it, you may need 3 objects (or compound shapes)
- Clipping mask shape
- Content to be clipped
- Base shape for appearance
You then use the top 2 to create a clipping mask. Then possibly group that clipping mask with the bottom object to retain the base appearance.
This is merely a cursory explanation. Without some images it's difficult to provide exact execution for any specific artwork.
From what I could gather, you perhaps have the clipping shape below content and are getting the wrong clipping.