You won't receive negative points on your credit card or your FF balance but the next $2,000 in charges will not accrue new points.

Example:
Month 1: Spend $3,000 get 3,000 miles.
Month 2: Return $2,000, spend $1,000 (You earn 0 miles. Miles from Month 1 were already reported to the airline and cannot be deducted by the bank)
Month 3: Spend $1,500 - you earn 500 miles on purchases since the $1,000 is still accounting for the $2,000 return.

Hope this clears things up. This is only true for airline programs. If it is a points program managed by the bank they may indeed be able to deduct points.