If it's useful for anyone, I did IGCSEs followed by Highers and I don't think it put me at any disadvantage at all. I'd missed two or three weeks in which they'd started the Higher courses, but that didn't seem to give me any problems. I had to read a section of the History textbook and catch up on a maths topic (it was only conversion into radians), but it honestly wasn't a big deal. When it came to essay subjects I can't really think of any way in which I was at a disadvantage, and I think I was significantly more confident with German than my classmates were.
I don't know how it would go the other way going into A levels, except that there's probably a significant difference in the way essays are marked (I actually really like Highers, but marking instructions for subjects like History can be a bit stupid. That problem seems to go away at AH level though).