Not a GeneratePress issue, but a client one! I have built a site around the Niche theme but forward changes the client has requested would make the Merch more appropriate as a base. So the question is, is there a simple or good way to go about switching these themes? Bearing in mind that the site is live.
If i had to do it i would create a Staging version of the site to work on.
Delete the Appearance > Elements and the Customizer > Additional CSS that Niche would have added.
Then perform the Merch Site import with Content, as it too uses Elements. Once the Import is done you will need to delete the additional products the site would have added.