IMHO, The use of thin plastic sheeting to seal a small koi pond sounds feasible. Not so much for a larger pond though.
I'm not sure of the size of your pond, but, your plan sounds very labor intensive; prepping the bottom, staging the cover soil, spreading the plastic, placing the cover soil carefully on the plastic, trenching and tucking in the outer edges of the plastic, using mats for the equipment, etc.
Your plan is to only cover the top portion of the pond with plastic. It seems to me that the water may migrate under the bottom edge and rise up the backside of the plastic, thereby rendering the plastic useless. Most lined ponds are 100% lined.
If the pond's sides have much slope at all, the cover soil will possibly slough/slide downwards towards the bottom as the pond fills, due to the cover soil not having any adhesion with the underlying soil. Likely resulting in the plastic being exposed to the elements, hooved animals, etc.
Provided you have clay of sufficient quality, it sounds like you have the equipment necessary to re-line and compact the entire pond, and be done with it.
Having all of that plastic semi-buried in the sub-surface of a leaking pond sounds like a nightmare scenario.
I feel your pain. Recently, I successfully re-lined my leaking pond (knock on wood) using only a small tractor with front bucket and box-blade. You gotta make sure you get good coverage on every square inch. Don't hesitate to apply over-kill.
Good luck, I hope you get it fixed.
