Its really not that complicated.
The amount your wife has to pay the home each month is assessed at the outset. This reflects her income and her assets and unless she availed of the loan scheme there is nothing to pay except the bill each month. After 3 years the value of her share of the home drops out of the calculation and so less has to be paid each month.
If she availed of the loan scheme, there is in effect a mortgage on the home. This increases by a monthly amount each year for 3 years, then it stops increasing. If you sell the house you will have to repay that amount.
To get any better advice you need to give more info. How long has she been in the home for example. What assets has she other than her share of your home.