Answer: identify chunks via something like rsyncs rolling window or GearHash, then name those chunks by Blake3. Trying to use Blake3's tree structure directly

Answer: identify chunks via something like rsyncs rolling window or GearHash, then name those chunks by Blake3. Trying to use Blake3's tree structure directly to dedupe is a misunderstanding of the problem you're trying to solve. Removing the counter would not let you use Blake3 alone for this purpose.