My thoughts for what they are worth:

Three inches seems a lot! How many gallons would that be? My calculation
is that 3 inches on your 12 x 20 pond would be very close on 450 gallons a
day. That is about 18 gallons per hour! That seems an unbelievable rate f
or evaporation, even from waterfalls!

You can check on the pond leaks pretty easily by stopping the flow and moni
toring whether the two ponds lose water at the same rate. If they do not,
one is leaking.

The streams and falls are harder. However, if you have leaks of that magni
tude (18 gal per hour), I suspect you would be able to see the puddles or e
ven the moisture in sand. Did you see them before the repairs? 500 gallon
s should show up somewhere!

We sealed our liner overlaps with roofing sealer not foam. The roofing sea
ler is designed to join liner (pond liner is the same as roofing). Foam is
rigid and subject to cracking, etc if not between rigid items like rocks.
Roofing sealer looks like tar and works like crazy.

Overall, I would be amazed at 18 gal/hour evaporation. I would search like
mad for leaks. Ponds first, then, starting from the bottom, add one link
at a time to see about loss of water. I would not sign off on the project
until I was sure about the 450 gallons per day loss. I would make him sign
a statement that he declares there to be no leaks, that 500 gallons per da
y is normal evaporation and that he will repair all leaks if that turns out
not to be the case. Unless you have a well, 450 gallons a day will surely
cost you an arm and a leg.

Best of luck!

Let us know how it turns out.

Jim