People will always have some bias to side with the person they know best. As people with high rep are known better, they will always have something in their advantage that a low-rep user doesn't have. That's just by nature of how humans work.
That said: Please realize that the flag-handlers do their best to try and address the actual problem, and to ignore who is talking against whom. There is a history here on MSE of very high rep users being rebuked and even suspended (for very non-trivial durations) because of the content of their comments.
I'm very sorry that you had a bad experience with those questions and that user, and I hope this doesn't discourage you from participating on Math.SE. I believe the user in question was somewhat upset that you did not notify him directly when you split the question (more on this in the section below). But, we must all remember to be nice (especially to the more recent members of MSE).
Regarding notifying people:
If you need to notify someone (for example, if you wanted to let someone called "userX" know that you are splitting a question), there are two ways to do so:
- Use an "@" notification in a comment. If you write "@userX I'm splitting this question", then userX gets a pop-up that says you notified them. However, if you just write "Hi, userX! I'm splitting the question," then they may never know that you were talking to them.
- The one exception to this is if you are commenting on one of their own questions/answers. That is, if userX made an answer, and I comment on that answer, they get a notification popup.
So, to be safe, if you are going to significantly change a question, notify the people (using a method from above) whose answer(s) may be affected.