I don't think you can get there with the counter on a USB-6008. It sounds like you need hardware-level timing for this DIO bit, so you'd need to use a more capable data acq device.
It isn't clear whether you need this to happen exactly 1 time or repeatedly every 2000 pulses. If it's every 2000 pulses, does it matter when/where you start the count? In other words, is the real requirement related to a position change that corresponds to 2000 pulses? If so, do you have a plan for establishing your 0 position to get the phasing right? Does your incremental encoder have 2 quadrature channels and an index pulse?
It's hard to recommend a daq board without knowing answers to these questions, and probably others as well. That said, the safest bet is probably a board based on the STC-3 timing module, such as X-series boards and certain cDAQ chassis.
-Kevin P
-- looking to hire? PM me...