For this sum, Alternating Series Test is not directly applicable because the magnitudes of the summands do not decay monotonely:

For the proof, it is convenient to group terms according to the value of $\lfloor \log_2 n\rfloor$. Indeed, for each given $N$, we may write
$$
\sum_{n=1}^{N} \frac{(-1)^n}{n} \lfloor \log_2 n \rfloor
= \sum_{n=1}^{N} \sum_{m=1}^{\infty} \frac{(-1)^n}{n} \cdot m \mathbf{1}_{\{ 2^m \leq n < 2^{m+1} \}}
= \sum_{m=1}^{\infty} A_{N,m},
\tag{1}
$$
where $A_{N,m}$ is defined by
$$ A_{N,m} = m \sum_{\substack{n \leq N \\ 2^m \leq n < 2^{m+1}}} \frac{(-1)^n}{n}. $$
Now we refer to the following intermediate observation in the proof of Alternating Series Test:
Lemma. Let $(a_k)_{m \leq k \leq n}$ be a sequence of non-negative and non-increasing real numbers. Then
$$ \left| \sum_{m \leq k \leq n} (-1)^k a_k \right| \leq a_m. $$
From this, we immediately find that
$$|A_{N,m}| \leq \frac{m}{2^m} \quad \text{for all} \quad N, m \geq 1. $$
Since this bound is summable in $m$, meaning that $\sum_{m\geq 1} m/2^m < \infty$, Weierstrass $M$-test shows that the sum in $\text{(1)}$ converges as $N\to\infty$. Moreover, the limit can be computed by taking limit term-wise:
$$ \lim_{N\to\infty} \sum_{n=1}^{N} \frac{(-1)^n}{n} \lfloor \log_2 n \rfloor
= \sum_{m=1}^{\infty} \lim_{N\to\infty} A_{N,m}. $$