If necessary league championship game. One out nobody on. Batter hits single. I tell umpire that he is a substitute that did not report. Umpire agrees and calls the runner out. He leaves the field. Next batter hits into 1-3 groundout for the third out. Defense leaves the field. Umpires conference and decide an incorrect call was made and the illegal substitution should have resulted in a warning and not an out. Umpires return illegal substitute to first base and allow batter that hit into 1-3 GO hit again. Rally ensues and team scores a run. While our team was hitting, I conferenced with my team and we decided we wanted to protest. I notified the umpire and the league commissioner. At the end of seven innings the game was tied 11-11. Top of the 9th inning opposition scored four runs. We failed to rally for the win. What should have happened with the protest?
What you have is a mess caused by the initial incorrect call if that's the rule your org uses (some orgs. are different.)and the following errors made by all.
Let's assume any US is only a warning in your league (org) and the umpires got together at the end of the inning and determined their initial call was wrong. They can invoke the "god rule" and "rectify any situation".....UNLESS another pitch is thrown or the pitcher and all infielders have left fair territory. So once a pitch was thrown to the next batter, in your OP the error in not correctable. But they did try to correct it, way too late. SN(The offense also needed to protest before a pitch to that batter (1-3 guy) or lose their right to protest but I don't see that in your OP.)
Once they tried to correct it (incorrectly) You had to protest before a pitch to the batter who hit into the 1-3 in the reset inning. After a pitch to him in the reset inning you lose your right to protest.
A number of mistakes were made here by the umpires, the offense who didn't protest when they should have and you guys who protested too late. By rule the protest is denied and the game is what it is.