Good question - Eric West recently posted that lime treatments will kill vegetation, but didn't expound on it much. No clue on the duckweed. Will you be excavating organics and silt from pond once it's drained? If so, removing a significant volume of organic material through excavation might cause the duckweed to stay away for good. It's certainly worth a shot to drain, nuke, and refill and see if it returns. If so, you can always treat later. What type of fishery are you planning on?