To define whether the new email is a new conversation or not, you could consider using a Condition. The Condition can be configured as Subject contains Re. If not, then it is a new conversation. Under the If No branch, add the next action to export the email then save it to SharePoint library.
Please take the following screenshot for a reference:
Currently there is no trigger can be used for “when an email is replied’, if you need this feature, please create a request on Flow Ideas Forum:
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