Johann, I'm not sure why you are asking this question... First of all, are you talking about a little run, or a constant motion, running 16ths? Either way sounds fine to me, as flutes and clarinets are very used to moving about wildly. Take a look at some Stravinsky. But, I don't understand why you would think this is hard. Maybe there's something I'm missing? But, if not, what you described is perfectly playable.
You are allowed to change key signature every now and then, you know!
Me? Most of my piece is in some sort of F, but it will always move out of F then come back. But I'm leaving all key signatures blank, as I like to write without key signatues, so I can use a more chromatic harmonic language.
Good luck with the rest of your piece! I'm sure it'll be great.