So here is what I know (I think).
She made an offer on a place that has a main house and a rental unit. Lender pre-approved them for a loan and associated down payment (that they can make) giving consideration to the potential rental income.
Things hit a snag because apparently the title does not include the rental unit. Supposedly the rental is permitted, but not covered/mentioned in the title. I've never heard of this before. Because of this, lender says they cannot give consideration to potential rental income. As a result, the down payment they want for the same total purchase price goes up to a level my sister cannot make.
So now the lender has approved a lower loan amount based on the original down payment which is not enough to cover the offer she made. She asked the seller to loan them the remainder. This is what she is calling the silent second. She says she would make monthly principal and interest payments on the second loan from the seller just like the primary mortgage. Seller would put a lien on the property after she enters escrow (would be subordinate to primary mortgage I think). Lender seems to be aware of all of this and cool with it according to her.
Lender says after two years of rental revenue, they could give her credit for the rental income despite the title issue and she could refinance the second loan. Seller declined this proposal, so maybe this will all go away.
I would never even think of doing something like this, but dying to hear some other people's thoughts.