If you want to whine about this, go to somewhere where Avid staffers occasionally turn up -
https://www.sibelius.com/cgi-bin/helpce ... &groupid=3. You will absolutely not be alone. We've all done it. However, in view of the fact that they are more concerned with getting sibelius to run on toy computers and have failed entirely to give PC and Mac uses any decent updates for the last 12 months don't hold your breath waiting.
How to solve your issue:
1. You will need to create two separate parts in the score (which will be hidden using focus on staves or by hiding the notes in the score and showing them in the parts.)
2. If you have been consistent in your use of div/unis/a1,a2/ voices etc the next step will be easy. if you haven't, then it wil be trickier.
3. Assuming you have been consistent, copy the music onto both new staves then, a section at a time, delete the music you don't need in each part. Consistent use of voices is your friend at this point.
4. You could try using explode to split the music automatically, but I have found it to be inconsistent and occasionally stupid.
5. Hide the extra staves in the score, delete the flute 1/2 parts using Parts-->delete parts to avoid accidentally printing them out.
6. Make sure you have numbered the new parts in the score (even though they're hidden) to be Flute 1 and Flute 2. I've forgotten to do this in the past and it causes no end of issues.
Alternatively - get Dorico.