There is a detailed post about creating 3D Clips For Prescription Glasses that addresses this precise issue.
The simplified version is: use a set of clip-on sunglasses, harvest the lenses from a set of theater glasses, pop the lenses out of the clip-on, use them as a template to cut replacements from the 3D glasses, and pop in your new 3D lenses.
Note: I'm comfortable wearing 3D glasses over my glasses so I have not used this technique.