Using $S_k(i)$ to indicate the $i^{th}$ term of $S_k$, then
$$S_n(j) = \sum_{i \le j} {n-k-1+j-i \choose j-i} S_k(i)$$ so you only need to do weighted sums over the original sequence.
Using $S_k(i)$ to indicate the $i^{th}$ term of $S_k$, then
$$S_n(j) = \sum_{i \le j} {n-k-1+j-i \choose j-i} S_k(i)$$ so you only need to do weighted sums over the original sequence.