Suppose, there is a duplicate question that has more up-votes than the original one, will it be removed after flagged ?
Should it be removed ?
I think this depends largely on the context of the questions. In general, duplicate questions are not deleted unless they are really, truly, exact duplicates down to the wording. Instead, duplicates with different phrasings or details are closed (but not deleted!) and linked to act as "sign posts" to original or more established questions.
Even if the new one is more heavily up-voted, it may still be closed if the older one contains more information or very useful answers. It's also possible for moderators to merge questions, but I'm not sure entirely how that plays out.
Really though, I don't think there's quite a hard-and-fast rule about how votes are considered when flagging duplicates, but rather content. If the content of the new one is better than the old one, then the old one may be closed as a dupe of the new one (and vice versa). This is sometimes the case with questions where the original is somewhat narrowly focused, but a more generally applicable question is asked that would benefit a larger audience. In that case it may make sense to close the older, narrower question as a duplicate of a more "canonical" one. If the content is very similar, I think it generally makes sense to simply close the new one to point it to the old one.
This is just my observational $0.02 on the matter, and I think that evaluating duplicates by content makes the most sense.