I've already proved that the above sum is $-n$ when $n$ is odd, but I'm having trouble proving the case for when $n$ is even.
So far I've done the following work:
Since $n$ is even, there exists $t \geq 0$ such that $n = 2^{t}n_{0}$, for $n_{0}$ odd.
Thus,
\begin{align*} \sum_{d \mid n} (-1)^{\frac{n}{d}} \varphi(d) &= \sum_{k=0}^{t} \sum_{d \mid n_{0}} (-1)^{\frac{n}{2^{k}d}} \varphi (2^{k}d)\\ &= \sum_{k=0}^{t-1} \left(\sum_{d\mid n_{0}} (-1)^{\frac{n}{2^{k}d}} \varphi(2^{k}d) \right)+ \sum_{d \mid n_{0}} (-1)^{\frac{n}{2^{t}d}} \varphi(2^{t}d)\\ &= \sum_{k=0}^{t-1} \left(\sum_{d\mid n_{0}} (-1)^{\frac{n}{2^{k}d}} \varphi(2^{k}d) \right)+ \sum_{d \mid n_{0}} (-1)^{\frac{n_{0}}{d}} \varphi(2^{t}d)\\ &= \sum_{k=0}^{t-1} \left(\sum_{d\mid n_{0}} (-1)^{\frac{n}{2^{k}d}}\varphi(2^{k}d) \right) - \sum_{d \mid n_{0}} \varphi(2^{t}d). \end{align*}
From here, if I can eliminate the $(-1)^{\frac{n}{2^{k}d}}$ term from the first sum, then the result follows easily since $(2^{t},d)=1$ for all $t$. I can't seem to find a way to prove that $(-1)^{\frac{n}{2^{k}d}}$ is always positive, however. If anyone has any ideas or could assist in any way (Am I even on the right track?) then it would be greatly appreciated, thanks!