Courtesy Runner/Substitution

[btdt]

Using a courtesy runner does not constitute a "substitution".
You can courtesy run for pitcher/catcher every time they are on base and the CR is not a sub, he is a CR.
Since they have not substituted for the pitcher/catcher when using CR your problem is solved if the umpires know the NFHS rules.
Also remember the CR can not have been in the game and after he is a CR he still have his original entry privileges.