Some conditions for a representation $999d_1 + 1000d_2 + 1001d_3 = N$ not to be unique.
If $d_2 \ge 2$, then $(d_1+1, d_2-2, d_3+1)$ is also a valid representation of $N$. For $N$ to have a unique representation, we must have $d_2 = 0$ or $1$.
If both $d_1 \ge 1$ and $d_2 \ge 1$, then $(d_1-1, d_2+2, d_3-1)$ is a valid representation of $N$, so at least one of $d_1$ and $d_3$ equals $0$.
If $501 \le d_1 \le 999$, then--assuming that $d_3=0$ because otherwise we already showed that there would be another representation--$(0, d_2 + 2d_1 - 1000, 1000-d_1)$ is a valid representation of $N$.
If $d_1 = 500$ and $d_2 = 1$, then--assuming that $d_3 = 0$ again--$(0, 1, 500)$ is another valid representation.
If $500 \le d_3 \le 999$, then $(1000-d_3, d_2 + 2d_3-999, 0)$ is a valid representation of $N$.
If $d_3 = 499$ and $d_2 = 1$, then--assuming that $d_3 = 0$ again--$(501, 0, 0)$ is another valid representation.
If either $d_1$ or $d_3$ exceed $999$, then we can subtract $1000$ from them and add $999$ or $1001$ to $d_2$, respectively, for another valid representation of $N$.
So what is the largest number we can construct that satisfies these requirements? For $d_2 = 1$, there are two possibilities, $d_3 = 498$ or $d_1 = 499$. For $d_2 = 0$, there are $d_3 = 499$ and $d_1 = 500$. These are $499498$, $499501$, and $499499$, $499500$, respectively.
If $499501$ is indeed uniquely representable (I claim that it is), then it is the largest.
Note that $N \equiv d_3 - d_1 \pmod{1000}$ from the equation at the top.
If there is another representation, then $d_1 + d_3 \le d_1 + d_2 + d_3 = \frac{N-d_3+d_1}{1000} < 499 - \frac{d_3-d_1}{1000}$. The largest $d_1$ can be is clearly $499$, and the largest $d_3$ can be is $498$. Because of this, to achieve $d_3 - d_1 \equiv 499 \pmod{1000}$, we would need $d_3 - d_1 = -499$. If $d_3 > 0$, then $d_1 > 499$ which is impossible.
Thus the answer is $499\cdot 999 + 1000 = \boxed{499501}$.