@gwillems I have it working now. I came across this link about theming and Flatpaks.
I ran the following.
flatpak --user override --filesystem=$HOME/.icons
flatpak --user override --env=ICON_THEME=Papirus
Now Gnome Calculator is getting the correct theme and it works when I apply the same to my other themes as well.
Thanks for your help and pointing me in the right direction!