I am going to CJS racing next week to get them to set my bike up on the Dyno, currently got the ECU-Unleashed flash which did remove the restrictions (the main reason I bought it) but it does not sort the fuelling with Arrow headers...
... ECU Unleashed and Off The Road both recommend a power commander to set a bike up for different exhausts, even Race Engineering who do the ECU-U Flashes reckon the bike is far better with a flash AND a power commander - both on the dyno and on the road, mainly because the flash does not sort out the closed loop fuelling and also because the flash is generic.
CJS insist they can sort my fuelling with the Arrow headers, as well as get the fuelling and ignition perfected, and will map each cylinder individually as well, all for less than the cost of a Power Commander - which is unable to remove the restrictions.
I have not heard of any issues with a flashed bike so far, but I would go somewhere that others have used regardless of if it is a flash-by-post or dyno setup.
I will post the results when I have had mine re-mapped by CJS, should be interesting to see if they really can better what ECU Unleashed did.