I am having a little trouble following your description of the pond setting, so please correct all of my wrong assumptions.
Is the pond basically a bowl in clay soil up to the pre-existing ground level, and then there is a build up of dirt that is above grade to make the final shore location and also even more dirt above grade for the site of the house?
When you say the pond filled back up about half way, is that water level about the same elevation as the original ground level? If so, then that makes pretty good sense that your "leak" is located where the previous owner built dirt above grade without performing the compaction necessary to make a pond.
Another test would be if you get a big rain and the water level in the pond rises several feet. It then would probably subside fairly quickly over the next few days, until it gets to roughly the current level, and the rate of water loss slows substantially. That would indicate the lowest level of your leak. (Can you affordably pump well water into your pond to perform a test of the leak rate and determine if there is a bottom to the leak?)
You can seal the sides of the pond by a method called creating a clay blanket. Even on a small pond, it would be fairly expensive because you would require proper compaction equipment. A pond liner will also be expensive.
I hope that helps a little as you continue evaluating your problem.
