Let's say someone who is currently inactive posted a question a long time ago, and it was answered. However, what if the answerer is incorrect, and the correct answer is posted later on, as shown here. Is it alright for me to flag it so that the BA is changed?
Yes. If all the conditions listed here are satisfied, then we will select the new answer. It doesn't matter who flags the post.
What if somebody posts something like this, an answer that is factually incorrect, but there's nothing stopping you from using the Pokemon because it's not banned? The Pokemon included in the answer is completely unviable in Anything Goes and doesn't fit on any serious teams, while being outclassed by pretty much every single Uber and Zacian-Crowned. The answerer also put very little to zero research to support their answer. However, this is Anything Goes, so while it doesn't fit, there's nothing stopping you from putting it on a team. Do I flag this?
No. Incorrect answers don't break the rules, including when people post incorrect answers on old questions. If you think the advice is bad, you should down-vote the answer.
I don't consider whether Aegislash is allowed to be a distinction between allowing that answer and not allowing it. If Aegislash were banned, then the answer would be even worse and even more deserving of your down-vote.
Also, I've seen several instances of people not being sure of their answer. Should I leave it where it is, or flag it?
My approach to this is to say answers should be an attempt at completely resolving the question. If the person who posted the answer isn't sure of this themselves, then they probably shouldn't have posted in the answer box. So, yes, you should flag an answer like that so it can be moved to a comment.