If it's simply tuning of the fundamental pitch for a single note, you could micro tune the notes in real time with pitch bend events.
If the entire phrase is fundamentally out of tune, you can tune the entire patch with the main Aria Interface.

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If the sample is fundamentally in tune, but there are some overtones in the sample that you simply cant get to 'blend' in the mix to satisfaction consider trying:
Option A: Try using EQ to filter out the unwanted harmonic. If the built in EQ Aria provides per instrument isn't enough, don't forget the basic EQ in your DAW mixing desk, and if that's still not enough...consider using the multi-output version of Aria, and using a more powerful dedicated EQ plugin provided by your DAW.
Also run the passage in a loop while playing with the various filters and controls in the Aria Player controls section (the filters in particular). Sometimes just playing with the filters and fine tuning provided in Aria can improve the blend. If this helps, then you'll want to dive into understanding how to send controller (or CC) messages with your composition and playback software so you can make these fine adjustments within your tracks/staves. With tracking style DAW systems, it's pretty easy to set up controller lanes or tracks, and even assign these interesting controllers to sliders/pots on MIDI controller key-boards or wind jammers.
Finally, don't forget your room shaping tools. Sometimes using a wetter mix (more reverb) can go a long way to blending strident harmonics that stick out pretty harshly as a dry sample, but add much desired character when set 'further back' in the mix (less main volume, more FX send).
Again, if Sonar is as powerful as I envision it (never tried it, but I hear it's pretty awesome), don't forget that you can use a multi output version of Aria, and unleash the power of your DAW's effect plugins. This brings a LOT to the table, as you can then also add compression, chorus, delay, very complex equalization schemes, side chained effects...well...the sky is the limit on how you can further shape sounds. If you're into anything remotely 'pop', 'jazz', or 'filmesque' it's very worthwhile to start experimenting with what all your DAW can do

Option B: Try different patches...
Just as an example...
There is more than one flute sample set.
Solo with vibrato
Solo without vibrato
Plr 1
Plr 2
Plr 3
Each patch is fairly unique and based on a different set of samples. Trying a different patch (or set of patches) might smooth out the phrase in question more to your liking. It's also possible to use samples from more than one patch for a single phrase over multiple channels (I.E. using more than one patch for a phrase that spans two octaves...plr 1 for the higher octave, and plr 3 patches for lower octave).
If you're using a score package that doesn't support assigning different MIDI channels to individual notes, and find yourself needing to bounce tracks/channels to use multiple patches for the same part, it's a pretty common tactic to use 'invisible' staves to send notes to alternate channels with different patches/instruments assigned to them, while muting notes on the main 'visible' staff that are no longer needed there.
With a tracking DAW like Sonar, it's usually pretty easy just to drop notes into different tracks set to different channels during the composition stages, then later merge the tracks to a single normalized track or part (where midi event channels remain unchanged).
Finally, don't be afraid to mix and match instruments from other plugins or synths that you might already have. Even if it's just for short passages or even single notes. If GPO4 is your only set of sounds to work with, you might can supplement the library a little with the free Sonatinia Sample Set that works in Dimension Pro or with the Aria Player (
http://sso.mattiaswestlund.net/ ).
Hopefully these tips can be useful. I too sometimes find individual notes or ranges in some patches that just don't blend to my liking with a particular mix. If EQ can't fix it, I usually have good look just trying some different patches (or combinations of patches). The more I work with GPO4, the more I know which patches to choose for a given passage, as they all do have some pretty unique attributes to their timber and articulations for each range/note (The samples were made by different musicians, on different horns/instruments/reeds/bows, etc). In short....Solo or Plr 1 is NOT always the best patch to use for everything....so try them all to see where their strong and weak points are for a given passage or harmonic chord/cluster.
Credo