The question is not well-posed, as it doesn't specify how a "positive" is determined. You are trying to say, based on just the first $n/2$ bits, whether a particular item has been added to the Bloom filter. When you check the bit positions given by the $l$ hash functions, some of them will lie in the first half, and (unless you have been improbably lucky and all of them were in the first half) some in the second. Of course, if even one of those bits in the first half is not set, then you can immediately declare a negative. The question is what you do when all of them are set.
There are several options:
declare a negative. This would be foolish, as you'd almost always declare a negative. The Bloom filter's crucial property that you never have false negatives, only false positives, is destroyed.
estimate the number of bits set in the second half, and calculate the probability that the other bits are set. This would be better accuracy-wise, but this too allows false negatives.
declare a positive. If you want to maintain the crucial—almost defining—property of a Bloom filter, of not having false negatives, then this is your only choice.
With the assumption that you do (3), the analysis is as in the classical case.
Suppose, after the Bloom filter is created, that a fraction $q$ of bits are still empty (unset), among the first $n/2$. (So $q$ is some number of the form $\frac{r}{n/2}$, for $0 \le r \le n/2$.) You now test for an item which happens not to have been added.
For a particular one of the $l$ hash functions, the probability that it contributes to a negative is $\frac12q$ (the bit position given by the hash function should lie in the first half, and then moreover among the $q$ fraction of unset bits). [Or, saying this differently, the probability that it counts as positive is $\frac12 + \frac12(1-q)$: either in the second half, or in the first half and among the fraction $1-q$ of set bits. Either way, the probability of contributing to a positive is $1-\frac12q$.]
The probability that all $l$ of them count as positive is therefore $\left(1-\frac12q\right)^l$.
Now for the approximations. The expected value of $q$ is the probability that a certain bit is left untouched by all of the $l$ hash functions for all of the $m$ items: that is
$$ E[q] = \left(1 - \frac1n\right)^{lm} \approx \exp(-lm/n)$$
We can prove as in the usual case that $q$ is very strongly concentrated around its expected value. So the probability of a false positive is therefore
$$\begin{align}
\left(1-\frac12q\right)^l
& \approx \left(1 - \frac{\exp(-lm/n)}{2}\right)^l
\end{align}
$$
as opposed to the $\left(1 - \exp(-lm/n)\right)^l$ of the full-Bloom-filter case.