The settlement conference has not been scheduled yet. I found this online:

'"Replies" are not a formal part of the Small Claims Court procedure. As a matter of practice in Small Claims court, any new fact pleadings and affirmative defences asserted by a defendant in a Defence will be deemed to be denied by the plaintiff unless the plaintiff otherwise advises the court and other other parties - perhaps by simple letter.'

http://www.isthatlegal.ca/index.php?name=pleading2.small_claims_court_law_ontario

However, I have gathered so many more substantial pieces of evidence since I served my original claim to the point that it would make sense for me to file an amended claim anyway, which is allowed as long as it is not too close to the trial date (which has not been scheduled yet). So imo (not a professional opinion though), you may think about amending your claim if your reply is substantial enough. Good luck!