Mark Mandell - Gone Round In Jersey
In the questioner's scenario, he would apply the shellac, allow to dry, clean his gun, then follow with the waterborne.

The shellac gets cleaned out with the alcohol. However, before running a chemically complex compound like waterborne finish through the same gun, it is best to make sure that all of the alcohol rinse is removed to avoid conflict with the tail solvents and emulsifiers in the waterborne; depending on mere evaporation is not, in my view, "best practice" in this situation. As water is miscible with the alcohol which is hydroscopic, the water rinse does the best job of removal. Since most all wet parts in guns are now stainless steel, the water is completely harmless.

I also find it beneficial to first "wet" my gun with the carrier/solvent/diluent of the finish that I'll be spraying. Running a bit if alcohol, water, or lacquer thinner through the gun before filling with finish seems to make the gun easier to clean later.