roymunson:
If you were a client, I'd recommend you killing the upper pond as well. Make sure you kill it completely. With all the time and $$$ you will be investing in the bigger pond, you don't want any contamination. Killing it is cheap insurance, and the genetics in the upper pond should be refreshed anyway - too much growing potential has been lost. BUT if those species don't fit in with your stocking plans, have no regrets and make sure none will be alive to make it to your other pond.
Using the upper pond as a forage pond for the bigger pond is a good idea.
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