below is the reply from IB staff:
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Short stock collateral cash gets backed out from settled cash (along with futures risk margin) when arriving at the cash principal subject to interest. So the cash proceeds from short sales would debit against your settled cash.
For example:
Start with 1mm settled USD
Short 1.5mm worth of SPY (assume collateral value for simplicity's sake)
Cash = 2.5mm
vs.
Principal = (500k)
So if you were to then buy, i.e. 500k worth of US-T, that amount gets backed out again.
Cash = 2mm
Principal = (1mm)