We're trying to find the number in the $n_1+n_2$-th row and $k_1+k_2$-th column of the modified Pascal's triangle. Let's call this number $F\left(n_1, k_1, n_2, k_2\right)$ I'll do this by taking the number in the original Pascal's triangle and subtracting $f\left(n_1, k_1, n_2, k_2\right)$ from it. Our job is to find $f$. Then, $$F\left(n_1, k_1, n_2, k_2\right)={{n_1+n_2}\choose{k_2}}-f\left(n_1, k_1, n_2, k_2\right)$$
Let's start by examining the example. Here's a display of the values of $f$, i.e. the difference between the original Pascal's triangle and our modified version.
0
0 0
0 0 0
0 0 0 0
0 0 0 4 1
0 0 0 4 5 1
0 0 0 4 9 6 1
0 0 0 4 13 15 7 1
Fixing $n_1$ and $k_1$, we see that $f$ sort of acts like Pascal's triangle in that
$$f\left(n_2, k_2\right)+f\left(n_2, k_2+1\right)=f\left(n_2+1, k_2+2\right)$$
Interesting. Intuitively, this makes sense. The cell $(4, 3)$ is 4 less than usual, and $(4, 4)$ is 1 less than usual. It follows that the cell $(5, 4)$ should be 5 less than usual, just because that's how Pascal's triangle works.
Let's take it one step further and "dissect" this mangled Pascal's triangle for $f$. What happens if only $(4, 3)$ is replaced with 0? What about if only $(4, 4)$ is replaced with 0?
4 0 0 1
4 4 0 0 1 1
4 8 4 0 0 1 2 1
4 12 12 4 0 0 1 3 3 1
Only replacing (4, 3) Only replacing (4, 4)
Well, I'll be darned! It looks like each number in row $n_1$ to the right of $k_1$ creates its own mini scaled-up Pascal's triangle, and they each add together to produce the triangle $f$.
Now let's generalise. Consider what happens when we replace $t_{n_1,k_1+i}$ with a zero. Then, another $n_2$ rows down and row $k_2$, the number is reduced by
$${{n_1}\choose{k_1+1}}{{n_2}\choose{k_2-k_1-1}}$$
Generally speaking, replacing a number $i$ rows to the right of $\left(n_1, k_1\right)$ results in a difference of
$${{n_1}\choose{k_1+i+1}}{{n_2}\choose{k_2-k_1-i-1}}$$
So, we can construct our final function as follows:
$$F\left(n_1, k_1, n_2, k_2\right)={{n_1+n_2}\choose{k_2}}-\sum\limits_{i=0}^{n_1-k_1}{{n_1}\choose{k_1+i+1}}{{n_2}\choose{k_2-k_1-i-1}}$$
I'm not sure if there's a way to reduce this any farther. It looks like it works with the provided example, although I haven't tested it against other cases yet.