Sorry to report here but here the fix for the problem seems simple. But from the beginning. External HDDs are mostly made with SMR technology. This means that they have a small CMR buffer in which they can do 32 KiB writes directly. When this buffer fills up, in order to write 32 KiB, the firmware of the drive must read e.g. 512 KiB in the SMR part, just like in an SSD without trim, and write them again with the changed 32KiB. Duplicacy, on the other hand, for a large backup writes these 32 KiB hundreds of thousands of times. Depending on the quality of the HDD firmware, this even makes it impossible to complete the backup. The solution seems to be to write 1MiB in one operation. Example patch here