Interesting high school play

[CecilOne]

I'm not even going to try looking this up.

1) I agree R1 would have to return if there actually was an out.
2) We consider a runner who has passed a base to have reached it, unless the defense appeals. So, in this case the BR is safe unless the defense appeals.
3) There is a rule that an injured player who can not reach a base may be replaced for the duration of being on base before going short-handed. That was not intended for CR, but you might use it.
4) I can see however, that the PU can refuse to accept a lineup change while the play is still on and runners are required to touch awarded bases.
5) If it were me, I would apply "the CR may run for the pitcher at any time". The pitcher can not be out for abandonment on a dead ball when already replaced by a CR or other sub.

This is one of those situations that the rule about umpire-in-chief can rule on things not covered is all about. But if the PU rules an out, "things not covered" still applies.