Let me assume that $m$ is even, for the moment. We can then rewrite your identity without any minus signs like this:
$$
\left[\binom n0+ \binom n2+\dots+\binom nm\right]=\left[\binom n1+\binom n3+\dots+\binom n{m-1}\right] + \binom{n-1}{m}.
$$
This rewritten identity can be proven using a bijective proof. Here are the combinatorial interpretations for each side of the equation.
LHS: Subsets of $\{1,\dots,n\}$ whose cardinality is at most $m$, and whose cardinality is even.
RHS: Subsets of $\{1,\dots,n\}$ whose cardinality is at most $m$, and whose cardinality is odd, OR subsets of $\{1,\dots,n\}$ with cardinality $m$ which do not include $1$.
To prove the identity, we just need to give a bijection between these combinatorial sets. To do this, given sets $A$ and $B$, let $A \oplus B$ denote the symmetric difference of $A$ and $B$. This means $A\oplus B=(A\setminus B)\cup (B\setminus A)$.
Given a subset $S$ of $\{1,\dots,n\}$, with even cardinality at most $m$, there are two cases.
If either $1\in S$ or $|S|<m$, then the corresponding set to $S$ is $S\oplus \{1\}$. Note that $S\oplus \{1\}$ will still have cardinality at most $m$, and the cardinality of $|S\oplus \{1\}|$ will be odd. Therefore, $S\oplus \{1\}$ is a set counted by $\left[\binom n1+\binom n3+\dots+\binom n{m-1}\right]$.
If both $1\notin S$ and $|S|=m$, then the corresponding set to $S$ is simply $S$ itself. In this case, the image of $S$ is one of the sets counted by $\binom{n-1}m$.
To prove this is a bijection, it suffices to give the inverse mapping. Given $T$ with odd cardinality at most $m$, the corresponding set is $T\oplus \{1\}$. Given $T$ with cardinality $m$ such that $1\notin T$, the corresponding set is just $T$. It is routine to prove that these two mappings are inverse to each other.
When $m$ is odd, an analogous proof works.