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Thank you, everyone!
I'm thinking rsync is going to be my best bet, then I can restore things as needed without messing anything up in hidden folders. I have a spare hard drive I can use as a lifeboat but should that be in ext4 or btrfs? Or does it even matter?
It shouldn't matter, but I would use ext4 for simplicity's sake. I bring that concept up again because if you can make a process more simple, it is obviously easier to understand and you'll then have time for the complexities that inevitably pop up. And they will.