If you are adding it to a sticker, you just need to use European_Flags-32.png
So if the person was from Russia, and emigrated to Australia (easiest example for me to use, as it was my aunt's father) you'd do this :
{{Migrating Ancestor
| origin = Imperial Russia (Russian Empire)
| destination = Queensland, Australia
| origin-flag = European_Flags-32.png
| destination-flag = Flags_of_Australian-5.png
}}