Thanks for the reply. Despite knowing the right way to do it, last month I was travelling through the highlands of Guatemala and was not able to find a radio trigger or sync cable before my capture session so here is the work around that I used:
1) I set the external flash to be 8x the power of the built in flash so almost all of the illumination was from the right direction
2) I used the built-in flash to wirelessly trigger the external flash for my highlight image capture sequence
This resulted in 2 reflections (one large from the external flash and a small one from the built in flash) on the reflective spheres. Since the built-in flash did not move, the reflection from it was always in the same place on the spheres which made it easy to paint out. This ensured that the right light position was calculated for the RTI.
3) After capture, I recorded a Photoshop action to automate the painting out the reflection of the built-in flash for the entire sequence. Every image received identical treatment.
4) Then I processed the RTI as per instructions after that.
I don't know if the added light from the built-in flash may have adversely affected the quality of the RTI, but we were very pleased with the outcome. Thanks for developing such a robust and useful technique.