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APFS is slower than HFS+ at present...and FW800 is slower than USB3 or Thunderbolt, so you have a relatively slow combo of devices...
When you say "nothing has changed", it still takes a while -- more than "seconds" -- to walk an entire folder tree and compare all the metadata for both drives - reading all that from the drive and literally doing comparisons. Why don't you send in the log when it's done so I can see the details?
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