First, note that the original integrand, $$\frac{1}{\sqrt{1 - x^2}} ,$$ is defined on the interval $(-1, 1)$.
Now, when we make the usual reverse substitution $x = \sin u$, there are many values $u$ that give a given value $\sin u$ so we must (usually implicitly) choose an interval for $u$ on which the function $u \mapsto \sin u$ is invertible and take on at least the values on which the original integrand is defined (per the above, in our case $\sin u$ must take on all of the values in $(-1, 1)$).
The usual (again, implicit) choice is $I := \left(-\frac{\pi}{2}, \frac{\pi}{2}\right)$. In fact, $\arcsin$ is defined to be the inverse function of the restriction $\sin\vert_{[-\frac{\pi}{2}, \frac{\pi}{2}]}$, so we can also make our choice of interval explicit by declaring $u = \arcsin x$. This choice of interval has the convenient property that for $u \in I$ we have $\cos u > 0$, so $\sqrt{\cos^2 u} = \cos u$ and hence
$$\int \frac{dx}{\sqrt{1 - x^2}} = \int du = u + C = \arcsin x + C$$
as usually claimed.
On the other hand, we could could have chosen another (less convenient) interval from which to take the values of our new variable, say, $\left(\frac{\pi}{2}, \frac{3 \pi}{2}\right)$, on which $\cos v < 0$, so that $\sqrt{\cos^2 v} = -\cos v$. In this case, the symmetry of the sine function gives that we can write this substitution as $v = \pi - \arcsin x$, and so
$$
\begin{align*}
\int\frac{dx}{\sqrt{1 - x^2}}
&= \int\frac{\cos v \,dv}{\sqrt{|\cos^2 v|}}\\
&= \int\frac{\cos v \,dv}{-\cos v}\\
&= -\int dv\\
&= - v + C'\\
&= -(\pi - \arcsin x) + C'\\
&= \arcsin x + (C' - \pi) .
\end{align*}
$$
By absorbing $-\pi$ in the constant, i.e., setting $C := C' - \pi$, we recover the answer we produced using the usual choice of interval.