There’s a little icon on comment replies in your inbox that will mark as read. In the following image, it’s the fourth from the left. To get that to show, you need to long press to the right of the user (it can be a little tricky).

The button with the red circle marks the reply as read.

The button with the blue circle marks all replies as read.

Make sure you’re on the latest version of jerboa if you don’t see them (0.0.34)