First, lets break things down a bit. like how you are creating your clips ?
The typical work flow is to Drag+Select a region of a clip.
Then Right click on top of that selected region and choose= Region FX / Melodyne.
Once all my edits are complete, I "Bounce to clips" to free up more resources.
But this also makes the clip not editable in Melodyne anymore (Unless you make it a region FX again).
Which version of Sonar are you using ?