Ignoring the fact that what you're describing sounds suspiciously like a Maxwell's demon, I think the equilibrium would be at a higher pressure because helium escaping against an overall pressure gradient would be doing work.
In essence, at the boundary I think the rate at which helium escapes would not simply be proportional to the gradient created by the internal pressure and the exterior partial pressure, but I think would include a term involving the whole exterior pressure.
It's not a Maxwell daemon, it's just a device for which nothing but helium exists. In the ideal gas model it would indeed create almost vacuum but the second law of thermodynamics is not violated since the process is symmetrical. Pressure of helium outside is also almost zero.
This relates to the difference between how a real gas and how an ideal gas behave in this scenario.
The difference in this situation will be very small in my opinion, broadly because the gas molecules in the atmosphere still have comparatively high mean free paths and therefore won’t interact with the “escaping” helium molecules.
Ignoring the fact that what you're describing sounds suspiciously like a Maxwell's demon, I think the equilibrium would be at a higher pressure because helium escaping against an overall pressure gradient would be doing work.
In essence, at the boundary I think the rate at which helium escapes would not simply be proportional to the gradient created by the internal pressure and the exterior partial pressure, but I think would include a term involving the whole exterior pressure.