I’m using the 16mm scan as a base and aligning the 35mm to it. One problem I came across is the 16mm has duplicate frames here and there. I’ll check out the full-sized (I work reduced-sized for reduced-lagged) to see if the frame code increments on the dup’ed frame, too. And as you mentioned, the 35mm has groups of frames missing … just to make things more fun. 😃
BTW, what software are you using?