You were right, the identity is true. Set $S_s = \sum_{k=0}^s \binom{2n+1}{2k} \binom{n-k}{s-k}$. We want to prove $S_s = 4^s\binom{n+s}{n-s}=4^s\binom{n+s}{2s}$ by induction on $s$.
For $s = 0$, $S_0 = \binom{2n+1}{0} \binom{n}{0} = 1$ so the right-hand side is $4^0 \binom{n+0}{0} = 1\implies$ The base case holds.
Now assume $S_{s-1} = 4^{s-1} \binom{n+s-1}{2s-2}$. We want to prove $S_s$ satisfies this recurrence:
$$s(2s-1) S_s - 2(n+s)(n-s+1) S_{s-1} = 0$$
Let $F(s,k) = \binom{2n+1}{2k}\binom{n-k}{s-k}$. Using $\binom{n-k}{s-1-k} = \frac{s-k}{n-s+1}\binom{n-k}{s-k}$, we can express the recurrence as a single sum $\sum_{k=0}^s T_k = 0$, where:
$$T_k = s(2s-1)F(s,k) - 2(n+s)(s-k)F(s,k) = [2k(n+s) - s(2n+1)]F(s,k)$$
Now to prove that $\sum_{k=0}^s T_k = 0$, we define the telescoping sequence:
$$H_k = -(2n-2k+1)(s-k) F(s,k)$$
By expanding the binomial coefficients, we can verify that:
$$H_k - H_{k-1} = [2k(n+s) - s(2n+1)] F(s,k) = T_k$$
Summing $T_k$ from $k=0$ to $s$ telescopes the series:
$$\sum_{k=0}^s T_k = H_s - H_{-1}$$
Because $H_s$ contains the factor $(s-s) = 0$ and $H_{-1}$ contains the term $\binom{2n+1}{-2} = 0$, both evaluate to $0$. Thus, $\sum_{k=0}^s T_k = 0$, and our recurrence is verified.
Now we just substitute the inductive hypothesis into our recurrence:
$$S_s = \frac{2(n+s)(n-s+1)}{s(2s-1)} \left[ 4^{s-1} \frac{(n+s-1)!}{(2s-2)!(n-s+1)!} \right]$$
Simplifying the factorials yields:
$$S_s = 4^{s-1} \frac{2(n+s)!}{s(2s-1)(2s-2)!(n-s)!} = 4^s \frac{(n+s)!}{(2s)!(n-s)!}$$
Therefore, $$S_s = 4^s \binom{n+s}{2s}$$
and our induction is complete.
The telescoping idea is the Wilf-Zeilberger method and is really useful for proving things like this.