Let me attest to how damned heavy that rubber stuff is. A good 18x20 liner for a garden pond is about 300 pounds of the thick material, it is still sitting by my shed waiting for a "team" effort. I cannot imagine dealing with 3000 pounds or more of the stuff at once, while trying to weld it among other things.
I would get some more quotes on re-coring the dam. Seems pretty darned expensive to me. Exorbitantly so. For that price you could dig a really narrow ditch, toss in some rebar and concrete, and call it a day. No roots, critters, or minor floods would wreck your day from that point onward. Of course concrete is pretty pricey these days too.
