The $3,000 of capital loss is deducted from your income, not from your tax. It does not reduce your tax by $3,000. The reduction in your tax depends on what tax bracket you are in. For example, if you are in the 22% tax bracket, the $3,000 subtracted from your income would reduce your tax by $660 (22% of $3,000). If nothing else changes, you could reduce your withholding by $660.
Reducing the withholding should not cause any problems in future years, as long as you continue to have enough tax withheld to avoid an underpayment penalty.
