Refer to a recent post by Matt Hudson. Your speedo signal is taken from the rear wheel, so it will not be affected by different sprocket sizes. Any discrepancy that you have observed between speedo and sat nav would have been there even before you changed the sprockets. There is nothing to 'heal'. 5% to 10% fast is about the norm these days.
HOWEVER !!! Grrr !! I was riding last night and my engine management light came on. It was code 25, gear position indicator. I had read in other posts on this forum that this issue had arisen some time after changing the sprockets. I very much doubt that there is anything wrong with my sensor/ECU or wiring. But I think that the factory mapping is noticing conflicting information from its various speed sensors, i.e. The rear wheel speed sensor is not tallying with the engine speed sensor, for the gear as indicated by the position sensor. DRAT! I very much doubt that there is anything we can do to swerve this problem. By changing the sprockets, we have deviated too far beyond the calculated parameters mapped into the ECU.
So, very reluctantly, I might have to change back to standard 15/44 sprockets, even though I much preferred the longer gearing of my 16/41. I will probably do it in stages, 16/44 initially, then if that fails I will revert to standard 15/44. Disappointing.