apply_surface(x, y, sprite, buffer);
SDL_Flip(buffer);
// ...
while ( !done )
{
    // ...
    y = y+1;
    // ...
}

Think of it this way:  Does changing the amount of sugar in a cake recipe change the sugar content for all cakes baked with the same recipe?  Of course not; the cake needs to be re-baked every time its recipe changes.

apply_surface(x, y, sprite, buffer);
SDL_Flip(buffer);

.
.
.

while ( !done )
{
    .
    .
    .

    y = y+1;

    .
    .
    .
}

Think of it this way:  Does changing the amount of sugar in a cake recipe change the sugar content for all cakes baked with the same recipe?  Of course not; the cake needs to be re-baked every time its recipe changes.