A clone is just a rasterized version of whatever object or objects that are cloned.
The problem you're faced with is complicated. You apparently have multiple clones representing the same source. You can eliminate the duplicates (keep the original), but you'll lose the positions and animations they occupy.
My advice: take a New Drop Zone for each duplicated clone. Place them right above the clone in the Layer List. Select each duplicate clone right underneath it in the layer list and in the inspector, click and drag on the Transform (title bar) and drag it onto the drop zone in the layer list. All Transform properties (including keyframes) will be copied to the Drop Zone. Check the animation and if there's Blending or other types of keyframed animation, then do the same thing for each of those property sections. Once you get all the animations copied over, then you can delete the "excess" clones.
Good luck... go slow... be thorough... save as a different name! (If you make a mistake, always make sure you have an original version to fall back on.