Can there be a loss of a gain of atoms in the world?

That depends on weather or not the quantum vacuum flux is real or not.

What the quantum vacuum flux means is that electrons pop into and out of existance constantly, if this is also true or protons and nuetrons then it is likely that the number of atoms in the universe is constantly changing

I think it stays the same, with the conservation of the mass and all of that mumbo jumbo.

E = mc^2

The number of atoms can change. Larger atoms can deteriorate into numerous smaller atoms. Atoms can be turned into energy.
The sun is changing the number of atoms by turning hydrogen into helium using nuclear fusion

http://en.wikipedia.org/wiki/Nuclear_fusion

Well if we are considering the whole universe it is growing, because I suppose there were no atoms during the start of big bang since electrons weren't held in orbit by the nuclei until some many years after.

http://en.wikipedia.org/wiki/Chronology_of_the_universe#Recombination

So it is not constant.

Thanks for the heads up.

I think what you may be wanting to ask is, "Do Protons decay?". And the answer to that is, "nobody knows". The standard model predicts that they do NOT decay, however certain Grant Unified Theories predict it does. But nobody has ever observed a proton decay event.