I wanted to say "Welcome back to your home country!" but I'm not sure if this is correct. Should I say "in" instead of "to" or is there a better way of saying this?
Definitely not "in" - "to" is the correct word. Unless it's significant that their "home" (as opposed to their "home country") is somewhere else, just "Welcome home!" is the right phrase. If you do want to separate "home" from "home country" then something like "xx welcomes you back!" could do it where xx is the country.