Have you tried Color Stabilizer (under Effects>Color Correction)?
If that doesn't work you'll have to resort to multiple layers, rotoscope, and a bunch of other work. From your description of the problem it sounds like the solution will be multiple layers with areas of interest masked.
That's why I always shoot a test first, always do stop motion with the camera set to manual exposure, and all other auto gain or color correction turned off.
Thanks for the reply.
We did extensive testing before the shot, since this couldn't be redone. The mistake was buying a new and untested lens relying on Canon and the fame of L lenses.
Next time I have to use this lens I'll put in a grey card which I'll crop out.
The camera was set on manual and raw. The development was focused on reducing small changes by pulling shadows and highlights.
The mishap was the new lens which didn't open and close reliably at F8. Meaning there where small differences in the opening at F8.
Like I explained Color Stabilizer won't work because of the lack of black or midpoints.
Forget all of the above
I just realized I do have a black and grey point.
When I cropped from 2*3 to 16*9, I cropped out a black tripod leg with a grey wheel.
But before I do another export of +10k raws, can you use the color stabilizer on just a black and grey? I do have higlights but they are never in the same place and never get exactly the same lighting.