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Hrm thanks Kev. I should have thought about 2. I didn't see any obvious way to remove points on the tree I'm using (Rednaxela) but it looks like it does support a max size! :facepalm how did I not notice that before? Sigh. Always the simple things!
Edit: Update, looks like the 2nd gen tree supports max size, but the 3rd gen tree, which I'm using only supports setting the bucket size and has no removal of old points. I'll have to check out other KD tree implementations to support limiting tree size.