Hey I am actively using Instantly with Hubspot, you can do two things to sort the issue. First you can directly integrate Hubspot with Instantly. In Instantly there is an integration to log the emails in Hubspot and as soon as a reply comes, tell your sales team to take over response at only one of the place. Logging emails from instantly to Hubspot is possible but vice versa not, so Hubspot will be the main channel to see all the conversations.
Second on order to mark the lead status of replies in Instantly and Hubspot you need to use Zapier or Make to create automations. As soon as a lead is marked as positive in Instantly, that automation will mark the lead as positive in Hubspot. You can do this for any lead status like negative or neutral. You will need to create custom field in Hubspot in order to do that.
Let me know if you need further help. You can DM me.