Illegal subtitutions

[The R]

During the 1st quarter the visiting team notifies the official scorer that they had three players (A9, A10, and A11) that showed up late that weren't in the book. I explain that we can add them but the cost is a T. However if they don't play there is no penalty. (I went over this with the coach as well).

A9, A10, and A11 play the last minute of the 2nd quarter. The table doesn't notify us that these are the three that weren't in the book.

During halftime the official scorer explains that A9, A10, and A11 were the three that were missing in the book and the three that just checked in. She also notified us that she had already added their numbers to the book as well.

This is similar to 3.3.3 Sit C however the difference is that the official scorer already made the change to the book.

What would be the correct ruling at this point?