However you do it, make sure to have the ECU zeroed out before the tune if you plan on importing the map to the ECU at some time in the future.
For instance, if you have Map x on the ECU (instead of 0 map), then dyno tune to modify the PCV, it'll make the changes as a difference to what is currently coming from the ECU, not from base. So then if you import that to the ECU later, it will be all messed up because you'll overwrite the base map with a correction map. For example, if the base map is +5 at some point, and the dyno needs +7 for optimal performance, the PCV will be +2, not +7, so when you import it back to the ECU, you'll have +2 (wrong) instead of +7 (correct).
If you're only having it flashed once then any mods will be done on the PCV later, it shouldn't matter since you're never changing the base map again.
2009 Yamaha YZF-R1
-Graves Cat Eliminator Carbon/Ti Exhaust, Frame/Clutch Sliders, Smog Block Off Plates, Front Sprocket Cover
-Flash-Tuned ECU, Dynojet PCV
-Fender Eliminator, LP flushmounts, OEM Seat Cowl
-Ballistic Evo2 8-cell battery
-ASV C5 Shorty Brake/Clutch Levers (blue), Renthal Dual Compound Grips
-Zero Gravity Corsa (light smoke)
-Goodridge SS brake lines
-Driven 520 conversion 16/45, RK GXW Chain, Probolt Sprocket Nuts
-GBRacing Case Covers, Vortex rearsets