As I understand your question, you are saying that you do not believe you have affirmative defenses to the complaint as currently drafted. You appear to believe the complaint needs "clarification" although you haven't moved to dismiss it. You believe that if the complaint is amended that you would then possibly have affirmative defenses.
First, don't count on the other side amending their complaint. If you haven't moved to dismiss it, then they may not. If you wish to add affirmative defenses to your answer, then you need to move (i.e., file a motion with the court and set it for hearing) to court to allow you to amend your answer to state affirmative defenses. Leave to amend is liberally granted in Florida.
Second, yes, if the other side amends, then you are allowed to file an amended answer and to add affirmative defenses at that time.
Third, yes, an amended pleading supersedes (i.e., entirely replaces) the previous pleading and stands on its own. They are not considered together.
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I wouldn't wait to amend your Answer to add affirmative defenses. What if the plaintiff doesn't amend the complaint? You're left with no affirmative defenses. If you served the Answer within the last 20 days you can amend without leave of court as long as the case has not been set for trial. Good luck.
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You can also file a motion seeking to amend your answer. These are commonly granted. You will then be able to file your amended answer and affirmative defenses. You can and should attach the amended answer and affirmative defenses to your motion. In Florida this is generally required.
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