A more elaborate counting argument.
More generally, let's take a $d$-dimensional checkboard of size $n_1\times\cdots\times n_d$ with the rule that we may flip coins in any hyperplane parallel to a coordinate hyperplane. Initally all coins are heads up. The natural questions to ask are:
Question 1. What are the possiblities for the number of heads-up coins after performing some moves?
Question 2. How many configurations are possible?
Note that, by inverting all hyperplanes in a certain direction, we invert the entire cuboid, so it is equivalent to ask how many tails we can have.
The operations commute and are involutions, so we may suppose no hyperplane is inverted twice, and a resulting configuration is then determined by the inverted hyperplanes. (But may be obtained in $2^{d-1}$ distinct ways; see below.) Say $a_1,\ldots,a_d$ hyperplanes are inverted along each of the directions.
The number of heads-up coins is then
$$\sum_{\substack{S\subset\{1,\ldots,d\}\\|S|\text{ even}}}\prod_{k\in S}a_k\prod_{k\notin S}(n_k-a_k)\tag1$$
(the number of coins flipped 0 times, twice, four times, etc...)
This equals 1
$$\frac12\left(N+\prod(n_k-2a_k)\right)\tag2$$
where $N=n_1\cdots n_d$.
We conclude that:
$H$ heads can be obtained iff $|2H-N|$ can be written as $b_1\cdots b_d$ with each $b_k\in\{0,\ldots,n_k\}$ of the same parity as $n_k$
In particular: 2
If $n_1=\ldots=n_d=n$ is even, then $2^{d-1}\mid H$.
To answer the second question, note that we're considering an action of $(\mathbb Z/2)^{n_1+\cdots+n_d}$ on the coins, and the orbit of each configuration is $2^{n_1+\cdots+n_d}$ divided by the stabilizer of (for example) the initial one.
The order of the stabilizer is the sum of the $\prod\binom{n_k}{a_k}$ over the solutions to $$N=\prod(n_k-2a_k),\qquad a_k\in[0,n_k]$$
Considering the absolute value learns that an even number of $a_k$'s equals $n_k$ and an odd number equals $0$. The binomial coefficients are all $1$, and we get $2^{d-1}$ for the order of the stabilizer:
There are $2^{n_1+\cdots+n_d-d+1}$ possible configurations, out of $2^{n_1\cdots n_d}$ in total. 3
A quick induction shows that $n_1\cdots n_d-(n_1+\cdots+n_d-d+1)\geq0$ with equality iff all but at most one $n_k=1$. So except for the $1\times\cdots\times1\times n$ cuboids, there are always unreacheable configurations.
1 Proof 1: Each term $\prod_{k\notin T}n_k\prod_{k\in T}a_k$ appears in $(1)$ with coefficient $(-1)^{|T\setminus S|}$ for each $S\subset T$ with $|S|$ even. By this, this gives $2^{d-|T|-1}$ for $T\neq\varnothing$, so we get the expansion of $(2)$ (see also second proof).
Proof 2: $$\sum_{\substack{S\subset\{1,\ldots,d\}\\|S|\text{ even}}}\prod_{k\in S}a_k\prod_{k\notin S}(n_k-a_k)=\sum_{\substack{S\subset\{1,\ldots,d\}\\|S|+d\text{ even}}}\prod_{k\notin S}a_k\prod_{k\in S}(n_k-a_k)$$
and
$$\begin{align*}\sum_{\substack{S\subset\{1,\ldots,d\}\\|S|+d\text{ even}}}\prod_{k\notin S}a_k\prod_{k\in S}(n_k-2a_k+a_k)
&=\sum_{\substack{S\subset\{1,\ldots,d\}\\|S|+d\text{ even}}}\sum_{T\subset S}\prod_{k\notin S}a_k\prod_{k\in T}(n_k-2a_k)\prod_{k\in S\setminus T}a_k\\
&=\sum_{T\subset\{1,\ldots,d\}}\prod_{k\in T}(n_k-2a_k)\prod_{k\notin T}a_k\cdot\#\{S: T\subset S\subset\{1,\ldots,d\}, |S|+d\text{ even}\}\\
&=\prod(n_k-2a_k)+\sum_{\substack{T\subset\{1,\ldots,d\}\\|T|<d}}\prod_{k\in T}(n_k-2a_k)\prod_{k\notin T}a_k\cdot 2^{d-|T|-1}\\
&=\frac12\prod(n_k-2a_k)+N/2\end{align*}$$
2 I believe direct combinatorial proofs of $2^k\mid H$ for all $k<d$ are possible as well, but become less elegant for $k>1$.
3 Again, I'm confident that a direct combinatorial proof exists (I have one for $d=3$).