Should I throw out batteries that had been discharged down to 2.0v?

Batteries and Chargers Rechargeable Batteries
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Here’s a test/review by HKJ that lists 2.0V as end of discharge voltage: Test/Review of Sony US18650VTC6 3000mAh (Green)

Based on that you’re probably OK. After watching plenty of videos of cells burning I’d pitch anything that discharges below listed tolerances.