OK, I don't know for sure but this is my guess, I think your right .. The chocolate gene was in the Yorkie parent. The F1 comes when you cross a traditionally colored Yorkie to a full Biewer.. the pups (called splitters) would look like traditional yorkies. They would carry the Biewer from the one parent and I imagine, if the Yorkie parent had chocolate in the background or was a chocolate Yorkie, the pups would carry that gene too.. (sorry, I'm not to versed on the chocolates)
The "silver" coloring and the black coloring I understand as I have a sibling group of two female splitters.. one has very very dark black and vibrant golden tan, the other is more muted tan and silver/blue. If these girls are bred to full Biewers, some of the litter would still look like a yorkie while some would look like a Biewer and be a Biewer..
Hope that helps..
Diana