I do not believe so in wodeflow. Wodeflow is not that great for starting GC games anyway. I use the original WODE menu app (first homebrew app made for the wode) because when a game is selected it reboots back to the wii main menu and you can start it that way no issues.
This method also allows wii games to start properly that will not play correctly if started via wodeflow - like the Sam and max series.
To answer your question - cant be done in wodeflow as far as I know so when prompted or disc 2 walk to the console - press eject to eject disc 1 (assuming it wa not auto ejected) - then select disc 2 from the LCD. (when you select disc 2 ensure to keep hold right on the joystick for at least a few seconds / until you see disc two started
I recommend keeping disc 2 of a game in your favourites list on the WODE itself. Makes it easier to find if you swap discs OR to select disc 2 from the start
P.s. maybe, and this is a big maybe, change the game ID in the iso and it might show in wodeflow. (again, I do not use wodeflow for GC games.