Maybe you were asleep. Dr. Frank entire theory is dependent on votes being injected into the process. He never mentioned subtracting votes because that does not fit his theory. And that is the point of the article's fact check and why they are asking Lindell and Frank for an explanation. Sounds like a fair question to ask.
I was wide awake. Dr. Frank described how the algorithm was dependent on the available inactive registered voters lists that constrained the number of votes that the algorithm could assign. The algorithm did not inject votes it simply checked that there were phantom voters in the list that could be used as cover in case there was a later (real) audit before subtracting and adding, always from Trump to Biden. It basically diseffranchised Trump voters and diluted them with dead or fake people.