If you're only moving a handful of presets, you can also rearrange them within the PitchFactor itself. After the first long press on the encoder, your current bank number starts flashing [For example: BNK 45:1]. Turn the encoder knob to the destination bank [Example: BNK 1:1], and a second long press on the encoder saves it to the new location. It's a "Rubik's Cube"- type of approach. Press another switch to bail out of the process for NO SAVE.
Of course, the librarian uses more of a visual approach, You're using all factory presets, so you don't absolutely have to back up your current setup. In either case, though, it might be prudent to map out your strategy beforehand on paper, and back up the PF presets. Make sure that you have the latest firmware (3.5.0) and the latest FactorLib revision downloaded.
And while you're in the system UTILITY section (for the SW VER check and BANKS limit setting), you might want to experiment with the SOURCE setting. It defaults to pitch-tracking for the range and polyphony of a guitar. Depending on the type of woodwind or saxophone you're using, it may track better after selecting SYN LEAD or SYN BASS for a SOURCE value.
Just curious: Are you using a pickup or a microphone/ preamp setup as the input for the PitchFactor?