It takes huge numbers of energetic particles, at the edge of the atmosphere where it's relatively easy to liberate atmosphere, to have a strongly observable effect at all.

And EVEN then, we're talking about a trivial number of atoms when you consider the atmosphere as a whole.

The sad fact is the atmosphere is constantly loosing atoms just due to the fact that the speed distribution of a gas gives some constituents more than escape velocity and they do just that unless a collision occurs.

Down here near the surface, a collision always occurs. Up near the edge of space, not necessarily....

I'd worry about the sun becoming a red giant before worrying about running out of atmosphere....