How about this:
You have a lead guitar track, recorded at the bridge pickup with all the high end harmonics intact.
Insert an EQ into the FX rack and roll off the high end. As much as you want.
Insert Melodyne into the FX rack below the EQ.
Do your Melodyne editing.
When done, bounce to clip.
Then turn off the EQ.
All the high end harmonics restored?
Or should you turn off the EQ before the bounce?