Save you comments from Instapaper to Evernote. This will keep all the comments from one article in the same note. Note that the comment trigger doesn't seem to work when you add a comment to an existing highlight. Works conjunction with my other recipe on saving highlights.
Then
Append to note
This Action will append to a note as determined by its title and notebook. Once a note’s size reaches 2MB a new note will be created.
Explore more great ways to automate Instapaper and Evernote