Arxiv substantial text overlap after breaking up paper
While arXiv does not publish the exact details of their implementation, in their help section on overlap detection, they have to following notes that may be useful for you:


  Submitters can preempt the addition of a text overlap admin note by marking any known overlaps in advance in the "Comments" header (as long as the earlier appearance of the text has a coauthor in common): for example, "this article draws heavily from arXiv:x, arXiv:y," or "this article supersedes arXiv:z."


and 


  A submitter who believes that an admin note indicating text overlap has been incorrectly applied to their article should contact arXiv moderation with a detailed explanation or justification.


In short: if you have sections that are intended to be in common between B and C, point them out in the comments, then flag for attention from a moderator.