It needs to be done in the initial production. PETG= polyethyleneterepthalate glycol-modified, a copolymer of cyclohexane dimethanol, ethyleneglycol, and dimethylterepthalate. PET is a the polymer of dimethylterephalate and ethylene glycol. There is actually a different set of bonds along the backbones of the two polymers. They may not even be miscible in one another.
If someone has deeper knowledge please step in, this is all pulled off of reading PET's wikipedia entry.