I complete my drawing, now I want to align the entire drawing to the artboard. Great! How do I do that without messing up all my layers? If I group the objects to align them to the artboard, then they move to one layer, and do not move back to their original layers when ungrouped. I don't want that.
I don't know if there is a standard procedure. Normally I have to align my graphics manually anyway, because the calculated center often is not the optical center. And of course most of my stuff goes into InDesign - no need to center it on the artboard. Nobody will ever see it.
Why not just Ctrl/Cmd+A to select everything?
If you have specific objects to go together, instead of grouping you may select them and Select>Save Selection so that you can work on them individually and then at any time Select>[Your chosen name of selection] to select them together without moving them from their layers.