Could give a try to an already existing Merkle tree implementation #1
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Deleting a branch is permanent. Although the deleted branch may continue to exist for a short time before it actually gets removed, it CANNOT be undone in most cases. Continue?
Such as https://github.com/fmerg/pymerkle but this one doesn't seem to have enough reputation to be user-friendly and bulletproof.
Or could implement https://eprint.iacr.org/archive/2019/226/1597952251.pdf#page=28.