I believe that it is kind of like "adios" in Spanish. "Adios" is from "a dios" or "to God," blessing someone when you leave them. "Kwaheri" is the same as "kwa heri" or "for blessedness," again, blessing someone when you leave them. That could be slightly off, but the idea is that it is really two words run together to make one and, in Swahili, you can either leave them apart or run them together.
Kwa heri - literally "With luck" - or blessedness as you said :) So you wish the person all the best as they go, on their way.
Good point! I hope you get lots of lingots for pointing that out! I gave you one.
You say the whole thing, not the separate pieces, if you want to say "goodbye."