I also looked into rdiff and bsdiff, both of which support binary files, but both of them seem to just output a diff file, rather than doing any actual copying/synchronizing. This functionality makes sense to me, but is there a utility that can handle this automatically? I thought about using rsync for this, but it seems that rsync only checks the file based on size & timestamp or by checksum, rather than bit-by-bit, and a simple checksum won't tell you where there are 0s when there should be 1s. If the left file's bit is 0 and the right file's bit is 1, copy that 1 to the left, or at least keep the 1 on the right, if two-way synchronization isn't an option.If the left file's bit is 1 and the right file's bit is 0, copy the 1 over to the right.Ideally, I'd like to synchronize both drives as follows: A lot of these files are binary files too. So some files on the source are fully intact while their counterparts on the destination are not, while other files are fully intact on the destination while their counterparts on the source are not. Most of that data consists of binary files. However, the zero-filled spots are different on the two separate destination drives. I can only presume that these differences are being caused by the parts of the files that have been zero-filled where errors had been encountered during copying. I can only presume that the differences are going to be caused by those zero bytes, which seem to be located in different places amongst the data on these two destination drives. Now, I have two destination drives with near-duplicate data, except that some of the data on both of these destination drives is definitely different. The source drive had been failing, so I used dd to copy over the data to one destination (with options conv=noerror,sync which fills error'd blocks with zero bytes) and I used ddrescue on the same source drive to copy data to a second partition, and I've heard that ddrescue also fills errors with zero bytes. I've got some files on two different destination drives, copied from the same source drive.
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