Yeah as long as you at least copy your home user folder, then you’re golden. I plan for my root to be wiped at any given time, so my important stuff lives in my home. That’s why it’s super nice with flatpaks! I believe if you install as user and system flatpaks, I think they both install in home? I’d stick to installing as a user for flatpaks if you can, it’s the same end result anyways and I’ve never had an issue.