[Thebear124]

Should still work.
Alternatively you could just say the more expensive items didn't arrive, unless you were already doing that with the planned 6.
Good luck.

I was already planning on doing that. I am not sure wether to say if 3/6 items came in a box and 1/3 came in the other. Do you think that makes it too obvious? Or is it fine?

They're all still the same order aren't they? I'd just wait a day or two after they both arrive, contact them and say what items are missing from the entire order. Don't mention anything about what box it was suppose to come in.
Good luck.