Wat? Amethyst should be pulling your relay setup from your relay lists saved on relays. Uninstalling shouldn't affect that, unless your relay lists could no longer be found.

it should, but I had to add it back manually. Not a major problem because of the auto-complete search function. The bigger issue for me is my customisation over the two years; settings, emojis, look and feel. I'm back to a blank, clean UX now.