I'm having trouble understand what you are comparing (owning $1k vs. refund of $4.7k). The $1k owing case includes what entry for the 1099-B's? Not including them? Not include the first? Including them but no number in the first box 1e cost basis.
In general it is very hard for us to answer these "why did it change" questions without seeing the before and after returns, which isn't really feasible.
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