This might be a better example of what I'm talking about. Say we want to find the area of a sphere. The form we want to integrate is
\omega = \sin \theta \, d \theta \wedge d \phi
Now, the sphere ##\Omega## is a closed surface, so ##\partial \Omega = 0##. However, the coordinate patch ##\tilde \Omega## covered by the coordinates ##\phi \in (0, 2\pi), \; \theta \in (0, \pi)## is not a closed surface, and is in fact contractible. We have that ##\partial \tilde \Omega## is the union of the north and south poles of the sphere, and a segment of a great circle that runs between them.
Now, it so happens that
\omega = d \big( - \cos \theta \, d \phi \big) = d \alpha
so we can use Stokes' theorem. So
\int_{\tilde \Omega} \omega = \int_{\partial \tilde \Omega} \alpha = - \int_{\partial \tilde \Omega} \cos \theta \, d \phi
To integrate around the "cut" between the north and south poles, we draw a loop around it. On either side there is a vertical part where ##d \phi = 0##, and so these parts do not contribute. Then around the north and south poles, there are tiny circles, at which ##\cos \theta = \pm 1## and ##\phi## runs from 0 to ##2 \pi##. The tiny circles go opposite directions, so each part contributes positively:
- \int_{\partial \tilde \Omega} \cos \theta \, d \phi = 2 \pi + 2 \pi = 4 \pi
So you see, if you are careful about how you cut up a manifold, you can apply Stokes' theorem in all sorts of situations.
In this case, we took a closed surface and removed a set of measure zero to turn it into a surface with boundary. The reason this worked is because the form ##\omega## is smooth on the set of measure zero that we removed. If that were not the case (say ##\omega## had a delta-function-like contribution on the "cut"), then you would have to include an extra piece to account for that.