Well, the reason I ask the question is that if you only don’t want to use it, you may as well go the safest route and just “hide” it by booting into Linux by default. So it would seem like the Apple stuff is not there, without you needing to fiddle around with actually safely deleting it.
If you however still want to get rid of it then in your special case I would clone the entire disk bit by bit, so if anything goes wrong you can safely restore it, anytime.
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