There is no need to reprogram the ECU
This is for a couple of reasons:
The engine barely feels a difference
Contrary to what the name implies, a "free-flowing" intake impacts the pressure at the valve inlet and not the volume of fresh inlet air per cycle.
Here are the numbers to back it up:
K&N provide detailed test data for the Yamaha R15, which serves as a basis for the following assumptions:
Pressure before the air intake (at max. flow) = 14.636 psi
Pressure drop across K&N intake (low dust) = 6 in. H2O
= 0.217 psi
Pressure at intake valve inlet = 14.419 psi
Let's assume that the stock air intake is really bad and drops pressure by 14 in. H2O (similar to pressure drop across the K&N filter when it is really clogged with dust). Under similar inlet conditions, the stock filter would yield the following:
Pressure at intake valve inlet = 14.130 psi
So that's less than 0.3 psi difference. In terms of mass flow, the engine sees roughly 2% more air1.
In the absence of fueling correction, a stoich AFR would increase from 14.7 to 15.0. Lean, but not exactly anorexic. Plus...
Fuel-injection management corrects for minor changes anyway
Most fuel-injected systems are capable of making fueling corrections to ensure that AFR's are what they ought to be. What this means is that leaning out should not even be a concern.
1 - based on values from Wolfram|Alpha, assuming 25 °C ambient temp